1. Exit out of the game
2. Open up your World of Warcraft\WTF\<accountname>\SavedVariables folder
3. Delete FuBar_TrainerFu.lua and FuBar_TrainerFu.bak
4. Re-enter the game and re-visit all your trainers
This cleared up all my issues, but made me lose all my trainer data on all my toons until I re-visited them.
If you read my post immediately before yours, you will see that I did all of that and it is working. I, also of course, had to revisit the trainers. This is with the version you recommended, r56106.109. With later versions, it didn't work, only works with r56106.109.
Also, try r56106 and let me know if it has any of those issues. If it doesn't have problems then I'll just nuke StiviS' changes.
I just tried that version, r56106.109, this morning. Upon the initial login, I was still seeing the unneeded skills and spells, so I did delete my data. After visiting all the trainers again, I don't see any skills or spells listed that I already know, so it looks like that version does not have that particular problem.
I was using TrainerFu r50281.5 and it was working fine even since 2.4 except for on my Rogue it indicated that available to learn were Crippling Poison (Rank 2), Instant Poison (Rank 5), and Mind-numbing Poison (Rank 3) but I had trained for those already.
I just updated to r74302, but it still showed that I need those three skills. I wiped known skills using the TrainerFu menu item, then traveled to all the trainers. After visiting all the Rogue trainers in the whole world, it now indicates that I can learn the three named above, as well as eight more: Instant Poison (Rank 2), (Rank 3), and (Rank 4); Deadly Poison (Rank 2) and (Rank 3); Mind-numbing Poison (Rank 2); and Wound Poison (Rank 2) and (Rank 3).
These are all skills that I have learned already. It also now says I can learn Bolt of Silk for Tailor skills, but I know that one already.