Weird Windows Booting Issues On Athlons (Score 1)

I've been working on a 750 Athlon system with a Gigahertz MB and when I installed an All In Wonder Pro card in it, it started doing all sorts of weird things. I finally found that an incompatability with the CD Writer (none specific) had to be installed as a secondary master instead of slave. This resolved all glitches the system was having. This I found after re-formatting, re-installing with different options and other different cards. This was on a windows 98SE system. There seemed to be no problem under Linux at any time and this error appeared with or without Linux installed with LILO.