Poisoned_Core

Hmm. That's a tough one. The only thing I can think of is removing the truck might have messed things up. I'd check if the author of GBA Intro Editor specified any requirements for the ROM version, such as 1.0 or 1.1, then compare with your own. I think AdvancedMap will tell you what version you're using in the bottom left corner of the window. If all is well there, I suggest getting another clean ROM and only applying the "remove truck" to it, then check if it breaks. If it does, you'll have to find a different way to remove the truck. If it doesn't break, I'm not sure what's going on.

As a quick note, there are stand-alone patches out there for removing the truck and tutorials on how to change the start position of the player using a hex editor instead of a program like GBA Intro Editor. I personally use these alternative methods.

What are the property values of map bank, number, X pos, and Y pos, in your GBA Intro Editor? Also, did you actually add new additional map banks or maps to AdvancedMap or did just just replace (as in, redraw) already-existing maps?

You're game doesn't go black until after the Prof Birch intro, correct? You also said you removed the truck part from the game. Where is the player supposed to start instead of inside the truck?

What changes did you make specifically that you're trying to test? Sounds to me like something wasn't inserted properly and the game's startup sequence was botched.