My apologies for all the confusion! I first noticed this Boot Pal issue when I brought the Amiga to work to display. In my excitement to take up less space, I purchased a Gotek Floppy Emulator. The machine is running a real Kickstart 3.1 version. Also WB 3.1 is the OS installed (to continue testing, I disconnected the HDD to test this issue)
But yes, with no floppy inserted (original floppy drive), and I boot PAL, it boots to the purple KS "Insert Disk" screen, still in PAL (awesome!).
Not using any loaders - I physically removed the HDD. Just trying to boot disks and disk images.
I'm using a CRT, so it is much easier to tell when PAL is enabled (attached). I adjusted my CRT's V-Height so that NTSC has black bars, and when switched to PAL, it will fill the screen.
However, I am now thinking it is the particular software being booted. Using the Early Startup method, the Amiga stays in PAL to run Gem'X.
When I try something else, like Kefren's Desert Dream, (among certain others) it forces back to NTSC. Almost like my telling it to switch to PAL was just overwritten by the demo/intro/trackloader.
It's a bummer because most everything I want to run (Scene demos, games) simply will not run or run correctly in NTSC. On my A500 I began using an impossible to find command called Palcon by Nico Francis (If I remember correctly?) before installing a hard switch. Can't find that app anymore.
I may just have to try a different disk release when I see this happening (or find a sweet hookup on a PAL machine! 
)
Again, sorry for all the confusion! I just wanted to boot some games/megademos in the proper refresh/resolution. 
Some of your disks may be using the 'system-configuration' file. Have a look on your disks for this file. It usually resides in the root directory, but could be in L or Devs. You could edit them with a 1.3 Preferences editor (to change screen position, interlaced or not, colours, printer prefs, mouse prefs etc). I'm not sure whether pal/ntsc is anything to do with it, but it just may be.
Also, I recommend you start to use degrader to force pal or to force ntsc.
