I realize that this information is a little late, but hopefully it may help others in the future.
I also experienced an issue with potions disappearing, but in my case it was the poison ones only. So I'm not sure if this may apply to anyone else's problems, but this is how I dealt with mine.
After noticing my poison potions seemed to be coming up missing on my main character from time to time, and at first it seemed a bit 'random'. Then I noticed it only seemed to happen while I was crafting. Then I got to work on doing a few reloads to try a few things out.
Turns out when I was making a poison grenade, or flask, etc., it would use my poison potions when it had the icon for an ooze barrel (which is what I thought was being used) in the combine slot. (i.e. Ooze barrel + empty flask) So in other words, even with an ooze barrel in my inventory or on the ground next to me, and having chosen it as the source of the poison (I right clicked the barrel, then chose the other item) to make the items, it still ended up using my poison potions instead! So I removed all my poison potions and placed them in a nearby empty container, then proceeded to try again. This time it worked exactly as it should have, it made a poison flask by using the ooze barrel and empty flask. Problem solved. =)
Hope this helps a few people down the road.