Backwards Compatibility issue: When playing a 2.10 quest in build 346, picking up bombs from an enemy drop will change on the counter but they are not available to select on the subscreen. I have included a picture below so you can see what the subscreen looks like. I was testing with my own quest so if you need to test it out the link is in the signature.

Bombs are broken in older quests - build 346
Are you sure you're using the latest beta, and that you're using a pristine version of your quest from 2.10? I played through to the bomb room of the shore line temple and never had any problems.
This is exactaly the problem I had, only the exact OPPOSITE. bombs would be 0, but theyed show up in the subscreen in 337. And again I will say it was completely random.
Eg. start new game-bug(bombs). reset-start new game- no bug(no bombs). reset- no bug again? and repeat. and repeat. Hey, isn't this fun???
If I come across this again i'll let you know. I'm downloading 346 now.
I don't know when I did it, but I must have saved a file of my quest in one of the betas as some point. I tried testing this again in my 2.10 only file and the bombs worked fine. Not a bug.