Well, I usually just let it go through the screen that says "this product not sponsored by Nintendo" and then I get my menu of games. This was working before I flashed it.
Now, if I hit start, as you recommended, I get the cooler interface and I go to the MyGame icon, but none of the games show up in the menu; even though they are on the card.
Any thoughts?
Thank you.
The problem is quite simple here. You are holding "Start" while the M3 is still booting, which causes it to boot into the built-in Moonshell (called Extend). This will give you the slightly better interface and the MyGame option.
If you boot up holding Select, it will boot straight into the GBA menu. If you want to go into the Nintendo BIOS, you have to hold START + SELECT now.
What WraithGR was trying to say though was this : power on your DS without pressing anything. Wait for the normal interface to show up with 8 icons and THEN press "START". That should show the standard GameBoy bootup screen (with the cool 'ding') and then go into GBA mode. GBA mode only has 6 icons instead of 8, so you can tell them apart easily. Load your ROM from GBA mode and you should be good to go.
The soft reset is L + R + A + B. This shouldn't change after flashing your DS. Just make sure that your ROMs were written with the "Enable Real-time Save" option in the M3 Game Manager.