Posted the same bug just two posts above you xD
Did you try switching the two stacks around? If I remember to manage my inventory, I'll keep the partial stack second and the full stack first. It's a work-around, but it's annoying <.<
Oh my bad! i'm new to this community and i can't find a way to navigate efficiently through the sea of bug reports. i saw your post and you explained the occurrence of the bug better than i did.
I switched the stacks around and yes it did solve the problem. However, it can be as you mentioned quite annoying. I tried this in Version 1.04 on my MacBook. I'm unable to use my windows computer at the moment but I assume it works too since it worked on yours (: