Well, a sure-fire check if the mod is working would be mousing over a skill with level higher than 9 and accelerating time; normally even at level 10 you would see experience to next level slowly go down, higher levels are quite fast; if the mod is active nothing of the sort happens.
Then you could load up your game, open up the console (tilda key, above tab; just in case) and check if there are lines saying "MapComponentInjector: map already has RTMadSkills.MapComponent_RTSkillIncreaser" or "MapComponentInjector: adding RTMadSkills.MapComponent_RTSkillIncreaser" and "MapComponentInjector: success!", both of which mean the mod should be working now.
It's of course possible there's some other way their experience went down, but I haven't encountered any such mechanisms, and they likely wouldn't be the "natural degradation" the mod aims to disable.
Hmm... Are you sure they didn't go up a level? Character screen displays experience needed to next level, which naturally starts from zero after leveling up.
The injector update is recent, so just in case: check the version you have.