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For me it works fine in 1.1.2624. It might be something specific to win10. But I would firstly suspect something wrong with your installation or downloads, especially mentioning that JecsTools also work incorrectly. Could it be that you have cleared appdata folder after installation rather than before it? Or assumed that loading order is from bottom to top rather than top to bottom? Or it's Steam version tries to still use mods from other location than you think it should? Chances are low, of course, but it won't hurt to check.

And you can find your log in \AppData\LocalLow\Ludeon Studios\RimWorld by Ludeon Studios\Player.log, hopefully it'll help more.

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If people have worse overall performance with bulk operations (wich includes food poision chance), they will not use it.

If a feature like this is not used, it is clearly broken.

I never use "cheapest" stone floors. I prefer wooden ones, later changing them to "fine" stone. Does it mean that "cheap" stone floors are broken or useless? No, it's just my personal playstyle.
Personally I was using bulk cooking from several versions ago, there were mods with the same mechanics, and they were also used by many other players without such compliances. So, probably this feature is fine for most of them.

If I know the batch is bad, why can I not automagically throw them out? Or at least manually remove them? So it should not be calculated batchwise.

Because it's your cook who should know it, not you. You are god (more or less), they are not. And their competency level (presented as poisoning chance) is what matters. You can think that they indeed try to detect and fix their mistakes while cooking (and you should be thankful that the ingridients and time are not wasted), and if the resulting food is still poisoned, it's simply because they were not able to detect it. And if you want magic, you have dev tools.
And again, of course, you can't throw out a poisoned 1/4 of the soup pot hoping that the other 3/4 should be healthy.

On the other hand, when the random decides that the food should NOT be poisoned, all 4 meals will NOT be poisoned. Thus it doesn't affect overall % of poisoned meals. For example, if you have 1% chance to make food poisoned, and cooking 400 meals, you'll get 4 poisoned meals in average regardless of whether you cook them 1 by 1 or in bulk.

It can happen when used with mods affecting designators (namely RIMMSqol and Allow Tool, as I mentioned earlier, maybe some others); sometimes not by just having those mods active but depending on their settings or just after entering their settings page. In the latter case it can help to remove More Planning after changes made, then add it again (if simple restart is not enough).

Also it can be incompatibilities of RIMMSAssemble:

It seems like this mod is incompatible with various mods which includes Map reroll, Real Ruins, Configurable maps and more planning.

- from comments on its Steam page.

Is it possible to make Command Palette disappear after second rightclick (or whatever button it was set to appear)?

Some specific Royalty quests are not appearing when using some storytellers made for older versions of RimWorld, not inherited from BaseStoryteller (I found it with one fork of Rainbeau Flambe Storyteller, though there is another one without this problem). It can be solved either by adding this inheritance (just change its <StorytellerDef> to <StorytellerDef ParentName="BaseStoryteller">) or adding missing elements directly in <comps>. Better contact its author so they could make a proper update.
It's also possible to switch to one of standard storytellers temporarily, and soon you'll receive missing quest(s).

It's not that hard to keep all your base clean even in vanilla.
1. Sterile tiles are specially designed to counter filth in areas like hospitals, kitchens and laboratories.
2. Making 1-2 pawns to "specialize" in cleaning (setting it to higher priority), especially if you have some not very useful otherwise (or useful only on rare occasions, e.g. specialists doctors/recruiters/fighters - having no other skills high - can often have a lot of spare time, though it depends on your playstyle, of course), usually will worth it even if sometimes they run back and forth. The same is also useful for hauling.
3. Don't underestimate planning your base layout. Less your pawns go into "important" rooms, less filth they'll carry in. So, either make only 1 door in those rooms, or place them so pawns won't be tempted to go through without real need. You can even forbid temporarily unnecessary doors.
4. Pawns can spread many types of filth, thus the cleaner your base is, the easier it is to keep it clean. Build floors in all rooms, corridors and often-used walkways outdoors. Restrict animals from floored areas. Clean blood after raids as soon as possible, at least in frequently visited areas.

When it comes to mods, there is everything you asked, and even more.
TD Enhancement Pack - auxiliary, to let you have unlimited amount of areas and to hide some of them from colonists/animals lists. And much more.
CleaningArea - to choose an area to clean only there. It's better to be used when you usually have most of your pawns allowed to clean.
Cleaning Priority - to set priorities to clean in several areas. It's better to be used when you have only some of your pawns "specialized" to clean.
Work Tab - to have more precise control over pawns' jobs priorities. I prefer to raise cleaning priority for all pawns for a couple of hours before they'll go to sleep, 20:00 - 22:00. And similar for hauling.
Common Sense - to avoid cleaning snow when it's snowing or raining and, more importantly, to let pawns automatically clean rooms before/after doing most jobs there. And much more.
Doormats - filth will be removed from pawns when stepping on these doormats.
Path Avoid - to discourage pawns from walking on certain tiles (tip: mark entrance tiles to bedrooms/hospitals/freezers, etc. as "strong", and your pawns will prefer to go around these rooms rather than through if possible, except when their job destination is inside).
Misc. Robots (maybe also with Misc. Robots++) or some other mods to get robots (or other creatures, probably) that will make cleaning (and other tasks) instead of your colonists.
Dubs Bad Hygiene and some other mods add buildings increasing the cleanliness of the rooms.
[W] Clear Way - my old (updated now) humble micromod, attempt to slightly discourage pawns from stepping on filth.

Recently I was adviced to try A Petition for Provisions (Request Items) for such thing.

Rimworld Search Agency allows to set a min per-spot limit to transfer.
Other useful features exist in Storage Tweaks.

Is it possible to also show which creatures they have for sale? Getting some specific animals is often a main reason why I'd want to send a caravan.

I tried to remove Pick Up And Haul at all, but the problem still existed, so I suppose it was not caused by this mod. Then, I remembered another mod I liked to use, Please Haul Perishables, and removed it (I was using 1.0 version, so probably it wasn't working properly anyway). The problem disappeared! Then I quickly searched and found 1.1 update: https://steamcommunity.com/sharedfiles/filedetails/?id=2073818889, installed it (with Pick Up And Haul returned, too). Seemingly works fine (at least for now).

I had similar problems, and thought they disappeared after I recently switched to Jobs of Opportunity. However, later I realized it wasn't true. My suspicions about a couple of other mods also weren't fruitful, still can't track the cause and exact conditions. Sometimes I get PickUpAndHaul's right-click menu, sometimes no menu at all (even can't e.g. prioritize construction if some item is laying on the blueprint). Often it helps to make this menu to appear if I put stockpile or Home zone over "problematic" items, but not in 100% cases. It also appears if the pawn is drafted, so you can draft, pick item(s) and either manually send to stockpile and drop there or undraft and click in the inventory 3rd button near the item(s) to let the pawn unload automatically. Annoying, but at least better than nothing.

Unfortunately I still didn't learn C#, thus no real code

Congrats! Would like to try, but just today started a new colony in decently warm biome, so... later )

What about skis, btw?