At opened inventory you can multiply items. In config all Items are set for stackable up to size of 64.

How to reproduce:
Set a tool @ first slot - take an item and drop it with right click and you will add a tool and loose a dropped block.

This just occures by items that are not naturally stackable.

That is a strange thing to happen. Luckily my current test version does not do this. Right click behavior is still screwed up though so I'll keep this open for that.

your Bukkit version is?
Your plugin version?
Mey i can try to get more details.

I'm running my latest code. I was able to replicate your issue with the 0.7 jar. Just know that it will work with the next version that I release (which I'm trying to fix as many of these bugs as possible for).

I might get a test jar up after some more work tonight.

Version 0.7.2 is up. Check it out and let me know if you find anything.

Right click functionality was fixed in 0.7.2