When I join a channel (or a group of channels) from the Favorites dialog and it's set to join minimized, mIRC simply ignores that option and activates the channel window.

(mIRC 6.12, Win98SE, no scripts loaded when testing)

works just fine for me. i assume these are also checked for join on connect..
6.12 on winXP

Joining on connect works here too, though.
I don't know what's happening, but they're not minimized no matter what I try to change..

Hmmm... Are you saying that it doesn't minimize when it auto joins on connect? Or just when you do it manually? Or both?

No, I just said that the "auto-join on connect" option works. The minimized one doesn't work on both situations.