This is a known problem related to OS9, ATM/ATR, and QXP v3 and v4. It appears that people have different solutions (permanent and temporary), but what worked for me was:
1. Turn ATM from Deluxe to "lite"
2. Use Suitcase v8.2 to manage fonts
3. Use ATR to group font families
I still have a slight "stall" but nothing like I originally had. Here is a MacFixIt forum link
that has 100+ responses to your very problem. Quark is supposed to be working on a v4 fix.
Best of luck,