When TNT explodes where CH is currently regenerating another explosion, multiple random blocks will drop and not regenerate as normal. This problem has caused massive failure when our players have used multiple TNT after each other.

This only happens while regenerating. Tried to set the "join-nearby-explosions" setting to false, and it seems to have fixed the problem for now.

We are running Bukkit 1.5.2-R0.1 with CH 6.3.5.

I'll have a look as soon as I can. Thanks for reporting.

Ok, I confirmed it. I found an acceptable fix: explosions are not fused if one has started replacing its blocks.
This allows for the nice replacement in case of a stack of TNT and avoids the bug.