I'm having this problem today for the first time.
I have several plants, that are all on day 3, suddenly are wilted with red + next to insect/fungus, and when I click the poison bottle symbol, it tells me it pours the potion over the plant, but the gump doesnt show it up at all. The greater heals, strengths and water are all showing up as "used" on the gump, but not the poison or cure.
I read Doireann's post up there, and just tried that - chose the water icon on the gump, and targetted my bottles of poison, and then it shows up on the gump.
Really odd!
*edits to add* I just noticed it isn't only the wilted ones, it was all the one's I *thought* I had used the potions on before I realised too - almost like the potion bottles were bugged, cos as soon as I used the water icon and targetted the stack of bottles, from then on using the poison bottle icon on the gump works (or so far does anyway!)