Failure to boot

I installed a new 40Gb Maxtor drive and installed Windows XP Pro. System had only the one drive. No problems. I wanted to copy some files from my old hard drive a 20Gb drive as a slave drive using Windows 98SE. No problems. I removed the slave from the system and after turning on the computer I got a boot failure. After reinstalling the slave the system booted up OK. Is it possible that something was written to the slave that is needed for a boot? Or is there another possible fault?