Humm, I had a similar problem to that as well, are you using an Intel based processor or are you using a Cyrix based processor.
I bought the Mini ITX mainboard by VIA with the onboard Eden processor (Cyrix based) and I could never get WinUAE to work on it without hanging and lots of pauses.
There used to be a Cyrix switch on WinUAE but I beleive it was eventually dropped and no longer supported.
I eventually had to do my WinUAE on another Intel based machine.
Other things that causes freezes for me are thing like SpySweeper by WebRoot and other programs that seize control of your system while they scan every single file that moves on your system which often causes weird pauses.
Does your system hang on any other applications or emulators? That might be helpful in troubleshooting this out.
I hope some of this helps..
