Then there's the close to 25 other open windows I have besides mIRC (browsers, cmd windows, folders, notepad's, other instances of mIRC, trillian, etc)

This statement would make me wonder how you are determining that it's mIRC that has the bug/causing the problem.

Hmm.. let's do some math.. 75 channels + 6 status windows (1 per network) + 10 custom windows + 3 pm/queries = 94 windows in mIRC.
As you state that you have multiple instances of mIRC running, and if you have the same number of window per instance, and even if you have just one other instance of mIRC running, you're now up to 188 windows + the taskbar windows for all of those other applications, can quite quickly and easily hit the 200+ window mark.