Kikstart 3.9, Amiga 1200, and Video Mode

[Oldsmobile_Mike]

Since you mention 3.9, I assume you're talking about for system-friendly stuff.  Just change your screenmode in Workbench.  Is there some reason that you need it to be in PAL all the time?

PS - the double reboot with 3.9 is normal, that's what allows it to patch the ROM stuff.  Only way to get around it is to burn a custom 3.9 ROM.  If you didn't already know.  

[Oldsmobile_Mike]

I know there were quite a few games that I attempted to play that were completely broken until I switched to PAL.

I haven't had any problems with those when using WHDLoad to switch to PAL when needed.  Obviously your mileage may vary.