Funny, I just came to this forum to see if this was an old bug. I recently started to build up my seed collection so I'm growing plants the old fashioned way and couldn't figure out why I can't always apply greater poison potions. I don't have any issues with Greater cure. I don't use kegs, I use bottles but the bug happens with both. Simple but annoying workaround - move the bottles in your bag. I'm using the classic client so don't know if this makes a difference, but anytime I try to apply a potion and it doesn't work I just pick up the bottles and move them in the bag...then it works again for awhile. You could probably make some sort of macro for this but I'm too lazy to experiment.
As for what's causing the bug? I think it has something to do with id tags on the potion stacks. My botanist is also my alchemist and when the greater poison potions stop working I mix up a few more greater poison potions and they won't stack with the previous stack of "bugged" potions. Then when the new stack of potions stops working I make more, and those won't stack with the previous two stacks. You can taste ID the potions but they still won't stack, so you have to drop them in a keg and pour them out again. Or just do what I suggested earlier - move them around your bag to get them working again. I also have this problem with Greater Heal potions on plants but I don't use them very often. I've never had the bug with Greater Cure or Greater Strength potions. Weird, huh?