I checked the status window for any possible errors, there were none. I believed that was the problem to begin with but there were no '* /hadd: line too long' etc errors at all.
Echo'ing the hash table results returned only a few nicknames which hadn't rejoined, so they were removed, mIRC just decided to ignore it for soem reason.
1hr? I guess you don't know how long DALnet netsplits last :P It can be from a few seconds to many hours... That's why I didn't implement that in the first place, in case the table was wiped and then they decided to rejoin.
But I agree with qwerty and yourself, that this wasn't built for multi-channel/network support. Which I might do in the near future, as to eliminate that problem.