1. Check if your TV supports NTSC & PAL 2. Use Scart or S-Video for better picture
3. Certify you choose the NTSC for NTSC and PAL for PAL games (obvious, but sometimes you never now)
4. Swap Magic does not support DVD-9 (double layered DVDs), DVD-/+RW media so be sure you don't use those.
5. ALWAYS use quality media for the backups.
I'd have to go with eduardoh on this one. That really sounds like a NTSC/PAL issue. Alot of times, PAL discs will play in B&W on NTSC systems. Sometimes they won't play at all. That goes for standard DVD players as well.
You can't boot programs from your usb flash drive if you're using Swap Magic 3.6 or below.
Swap Magic 3.8 Coder, will give you that option.
Or you can install the indepenance exploit to your memory card, get a program called "launchelf" and name it BOOT.ELF in your BxDATA folder on your memory card, and use a trigger disk to load it.
(Launchelf is a program designed to boot other elfs - no, not those creatures you see in fantasy genres, Executive Link File, think of it as .exe's for your PS2.
Google this one up if your interested in running programs from usb (or your memory card, and any other form of storage the PS2 supports, including HDD). There are various installers around that you can use. They come (usually) as disk images that you just burn to a CD, and swap with your CD version Swap Magic.
Just keep in mind, this method means sacrificing an authentic PSone disc, because the method relies on a flaw in the way PS2 handles PSx compatability. When you set it up, it will ask you to insert a PSx disc so it can read the disc id.
After it's setup, when you boot from that PSX disc, the game won't load. Instead, Launchelf (or whatever ELF is named "BOOT.ELF" in your memory cards BxDATA system).
