That's surprising. If it definitely doesn't work on all banks then the BIOS must be corrupt, so you'll need to fit a chip.
And to reiterate what lordvader129 said, you don't use XBtool with iND-BIOS. I've just tried and it refuses to open iND-BIOS.5003, so I have no idea what you actually did. I suspect that you might have used X2ool, which is for X2.5xxx BIOSes, and which just writes an X2config.ini file, but that doesn't explain why the BIOS is corrupt.
You've also missed the key point about using iND-BIOS.5003, which is that you DON'T edit the BIOS, you flash the BIOS then make your changes in the config file, C:\ind-bios.cfg
This post has been edited by Heimdall: Sep 11 2010, 01:18 PM