Based on it's description, the "Pain is Virtue" meme has a set of conditions where the player is required to select one:
- Pain: Idealized OR Rough Living: Welcomed
- Comfort: Ignored OR Rough Living: Welcomed
- Slab Bed: Preferred OR Rough Living: Welcomed
What appears to happen is that when the religion is selected, the game will randomize the traits the player receives (I believe it can be as little as one "Rough Living: Welcomed" trait, or up to all four traits that are possible).
However, when the player manually adds a precept related to this religion they can no longer remove it even if they match the criteria. For example: If the player has "Rough Living: Welcomed" and manually selects "Slab Bed: Preferred" as a percept, it can no longer be removed due to being marked as being required. Even though the player still has the "Rough Living: Welcomed" percept that should cover the Meme's criteria.
Moderator Note:
This has been reworked since this post. As of 1.3.3087 there are now 5 required precepts for Pain is Virtue, and they are all mandatory.