It is a known bug that when learning new spells at your class trainer only your currently active spec is updated to use the new spell ranks. In fact there is an add-on, RankWatch, just to check for this. (Note: If you do use RankWatch use the '/rankwatch 80' command to have it only whisper people at max level. If you haven't fixed your spells by then you deserve a reminder.)
Anywho, the add-on lets you know there is a problem, but doesn't fix it for you. Worst case scenario you go through each action bar slot one at a time and check your spellbook for any updates. More than likely you just keep using the old ranks till your RankWatch add-on, or someone else's, tells you to update them. There is a better way, and it all fits in a handy macro you can use after training.
/run if not InCombatLockdown() then for i=1,120 do t,x,x,s=GetActionInfo(i)if t=="spell"then PickupSpell((GetSpellInfo(s)))PlaceAction(i)end end end
Obviously RankWatch should be updated to do this for you automatically when it sees you used a downranked spell the next time you are out of combat, but in the meantime this works nicely. :)