lostcalpolydude, did you find a fix besides modifying your behavior? I also have Mac OS 10.4.11, and mafia freezing has gotten to the point where it's actually faster to play my adventures manually than to have mafia freeze, logout, log back in, work a little longer, and then (sometimes) repeat the process. The problem may be intermittent, but it's really annoying. I don't think I finished a single day of Crimbo play without mafia freezing.
For me, the chance of freezing doesn't just happen with alerts - it happens sometimes if I have another application running that covers mafia (including the relay browser - Safari, for me) and I click back to mafia, if the mini-browser opens due to low HP from my actions while the relay browser and I close it (after clicking back to the main mafia application to cast buffs, eat, etc), or just sometimes when it finishes with a round of turns (this is a little different, though).
In the last case, mafia's GUI just freezes - I can see everything on the tab I'm on, the status bars for connectivity still track, but clicking anywhere on the GUI has no effect. I can still use the menu bar, and if I open the mini-browser and close it, I get the "freezing" effect I most commonly see. When mafia freezes (for lack of a better word - perhaps, becomes beige would be a better description), I can use the menu bar to open the relay browser, which will work; do the quests; or open hunter-type popup windows, but the tabs and lower right area of the GUI vanish into a blank beige area (except the button area and the green bar) and I can't navigate between tabs or use almost anything on the screen (I can select text areas - which appear out of the beige when clicked on - and, provided I had the foresight to leave it on the Graphical CLI tab before, successfully type in commands in the command line there).
I can't pinpoint when this issue started; early this summer, I think. I do know that it continued after I reformatted my HD & reinstalled everything in August (I think I used the v. 12.4 installer then). I've thrown away my KoLMafia folder once since then and tried almost every subsequent upgrade (I have 12.8 now) and the problem always reoccurs.
I can't figure out how to get around this (except by doing everything manually, but KoLMafia has a superior interface for a lot of aspects of play and I miss it). Should I avoid using any other programs while mafia is running (this hasn't worked well—it's how I found that mafia likely freezes before I get the beige screen)? Should I wait longer after it finishes playing a round of turns to click from tab to tab? Throw away the KoLMafia folder again? Suggestions, please?