I'm dual booting Knoppix hard-drive install (Debian) and Windows XP for a while and I had the same problem. Well, not exactly. A black line on the _left_ side of the screen appeared when I booted to Linux, so I removed it by adjusting the horizontal position of screen using the display controls (not using Toshiba, I have no idea if they have those). Every time I booted I had to switch them over again. Recently I installed nvidia drivers on Linux, and the black line appeared again (this time on the _right_ side), so I removed it as usual. But when I booted back to XP, I realised that the black line was gone. Well, what am I trying to say, is that the driver corrects the screen position back instead of breaking it. I also installed nvidia's drivers on xp, the black line didn't appear after the install. Linux just detects monitor settings somehow differently.
If this is completely not the case and totally off topic, I apologise