I don't know if anyone is still having this problem. I just installed Supernatural and updated to the 1.50 patch, so this is new for me. I created a Sim with the Alchemist LTW, so first thing I bought was an alchemy station. I tried to use it, and the action kept disappearing. I saw on this thread the thing about seeds, but he was a new Sim with nothing in his inventory, so that didn't fit. The indoor problem is probably a pathing issue, with something getting in the way even though it doesn't appear to be. (The same thing can happen with showers if they're not placed properly, if you think about it.)
So I removed my hacks, deleted my cache files, and tried again with a new Sim from my Sim Bin in an empty lot with just the alchemy station. Once again, the action vanished from his queue.
But then I decided to try again without any cc at all. I removed my cc (the non-hacks) and deleted my cache files and I was able to use the alchemy station.
Just letting any new person with this problem know, because it looks like there is some cc out there that will conflict with the alchemy station, and probably other things. It happened to me once before with the store spellbook, so in a way I'm not surprised. But if you've eliminated seeds (I remember the seed / fishing issue from a while back) and your station is outdoors so there's no pathing issue involved, try removing ALL of your cc and trying again.
Turned out to be a very old SimSlice object for me. Not sure which one, because since I don't use any of those objects anymore, I just deleted all of them.