Time for a lesson on flashme
Keys held when turning on a FlashMe'd DS (ANY version of flashme)
Start+Select boots using the protected NDS bootstrap (meaning you are force jumped to DS mode on the GBA bus via a stripped down passme type loader, it is there in case of "bricking" which can occur only on the "unprotected by SL1" portion of the flash chip).
Select disables the standard flashme patched boot from GBA slot (even when "PASS" is present in the GBA header), meaning that unless you have auto run on in the bios and the appropriate card in the DS that is set to auto run, you
will boot directly to the DS's normal menu
A+B+X+Y is to force the flashme passme type patch; when you have DS in the GBA slot and it doesnt have "PASS" as the GBA header flashme wont auto boot it, so you use these keys to force it to try and boot it in NDS mode.
FlashMe, in the DS's firmware (NOT BIOS, the BIOS isnt flashable on the DS!!) is not really affected by what card happens to be in the GBA slot, though it does check it to see if the "PASS" is present as the gamecode to see if it should auto boot it in DS mode. The DS's menu itself is essentially a DS app that is stored in a highly compressed form and flashed onto and loaded from a flash chip, somewhat like a PC's OS is bootstrapped from the HDD by the BIOS (HDD instead of a flash chip).
BTW: the button to press in M3's DS menu to get to GBA mode is "START", if you are not in GBA mode it will try to load the file like a DS ROM (it is not very intelligent, cant tell the difference between a "*.ds.gba" and a "*.gba"