Ok, something weird going on then. I checked the drop rate and they are dropping 1 at 50% like they should, however, because of the 10 charges of shrink on it they are actually dropping in stacks of 10. For example, I looted 5 drops of essence, but had 50 of them in my bag. When I did two combines, I then had 48 instead of 3.
*Edit* Now that they stack, just take the charges off. That should solve the problem.