EDIT: I've found a solution for playing NTSC games properly on PAL PS2 Slims.
Just thought I'd post an update for anyone having the same problem. This only seems to be an issue when using Breaker Pro with PS2 slims as I tried on my PAL Psone slim and Breaker Pro was able to change the video mode fine and play NTSC games full screen. But if you don't have a Psone to use, there's another way for PS2 slims which works for me.
So assuming you have a flip top lid, and Free Mcboot installed for your PS2 Slim get hold of an application for FMCB called PS1VModeNeg. Here is a link to download it.
http://www.mediafire.com/download/4xcoa42jm5h0ldo/[140721]PS1VModeNeg-0101-bin.7z
I assume you know what to do to launch it and everything so it's simply a case of
1. Load the app by browsing your memory stick you keep the .elf files on
2. The app will tell you to insert a disc so you need to actually eject the disc lid instead of just placing the disc through the flip top hole so it can register a disc is in the console
3. Insert your Breaker Pro close the lid so it registers a disc is in the drive and wait for it to load (every now and again it might say unsupported disc, I just open and close the lid and it works. It's probably my disc being scratched)
4. It should now load with the normal PS1 logo, but it will be off centre, this is what we want.
5. In the Breaker Pro menu, video mode doesn't matter when using it with a Slim PS2, but if you want you can just turn it to off anyway but it won't affect anything.
6. Click start game, take your stopped Breaker Pro disc out using your flip top hole, and boot your backup by pressing any button.
Game should load full screen/60hz. Assuming your backup is an NTSC version of the game. Hopefully someone else can confirm this method.
Good luck.
Just thought I'd post an update for anyone having the same problem. This only seems to be an issue when using Breaker Pro with PS2 slims as I tried on my PAL Psone slim and Breaker Pro was able to change the video mode fine and play NTSC games full screen. But if you don't have a Psone to use, there's another way for PS2 slims which works for me.
So assuming you have a flip top lid, and Free Mcboot installed for your PS2 Slim get hold of an application for FMCB called PS1VModeNeg. Here is a link to download it.
http://www.mediafire.com/download/4xcoa42jm5h0ldo/[140721]PS1VModeNeg-0101-bin.7z
I assume you know what to do to launch it and everything so it's simply a case of
1. Load the app by browsing your memory stick you keep the .elf files on
2. The app will tell you to insert a disc so you need to actually eject the disc lid instead of just placing the disc through the flip top hole so it can register a disc is in the console
3. Insert your Breaker Pro close the lid so it registers a disc is in the drive and wait for it to load (every now and again it might say unsupported disc, I just open and close the lid and it works. It's probably my disc being scratched)
4. It should now load with the normal PS1 logo, but it will be off centre, this is what we want.
5. In the Breaker Pro menu, video mode doesn't matter when using it with a Slim PS2, but if you want you can just turn it to off anyway but it won't affect anything.
6. Click start game, take your stopped Breaker Pro disc out using your flip top hole, and boot your backup by pressing any button.
Game should load full screen/60hz. Assuming your backup is an NTSC version of the game. Hopefully someone else can confirm this method.
Good luck.