I just setup and started testing stockable variants in vm 2.0.20b with joomla 2.5.11 and php 5.3.3. All seemed to go well and it appears stock is being calculated correctly. The drop down also is working showing tshirt sizes from small to 4xl and adjusting the price for appropriate items. Cart also is fine for the first item added.
The problem is when I attempt to add a SECOND tshirt to the cart. Instead of ADDING another shirt it REPLACES the first shirt and its requested variant (tshirt size).
HELP.
Well it appears I must be crazy because it stopped doing it all of a sudden. I tried logged admins, registered user and not logged it with a couple of different browsers and I can't reproduce it. Initially it did it about 5 times in a row may have been a glitch in the cart or something from switching from one type of item to another? Not sure....
I have exactly the same issue - is this known bug I cant seem to clear it unlike you have!!