from Early Startup, when I enable PAL and click Boot, the change reverts back to NTSC before the Floppy Drive or HDD is accessed
Probably a dumb question, but how can you tell? Just tested it on my Amiga's, when I click PAL and then click Boot, I get a black screen until the OS is almost loaded. At which point it comes up with a NTSC screenmode, because that's what I have specified in my ScreenMode prefs, but if I run SysInfo I can tell the system is operating at 50Hz (see attached screenshot).
Are you running a straight 3.1? Not anything like 3.9 or any of the "LoadModule" or "LoadResident"-type commands that can trigger a double-reboot, correct? (in which case you would have to select PAL on the second reboot)
Remind us again what it is you're trying to do? Specifically, what software are you trying to force into PAL mode?