dual sys w98 & xp hanging-up

I have most of W98 running smooth (85%), xp is a little worse (80%). IE6 (but it appears XP has IE5 on the users other than the administrator (me). Does IE6 get updated globally to all users and both partioned sides? Most of my problems stopped when I reinstalled the mother board on both partioned sides. Should I do it for both sides? I start both sides with selected startup, W98 only systemtray and explorer ?, XP mobsync and reboot. not sure if thats ok. I don't freeze on my desktop any more but I still do when going from one site to another or open too many windows.
My mouse (logitec usb) if I move it to fast seems to make it happen also, but that's prbly just me. Playing a data disk on media player is garbled but not on winamp? COULD USE SOME SUGGESTIONS. PLEASE post for W98's problem is in W98 forum, Thanks MinnesotaMike. and to the staff here. HD was formatted and clean install of W98. Xp was the same but WIN2000.

I think I've isolated it further. Now it seems to happen when I access morpheus or bearshare or the like. It seems that when the pop-ups load it freezes my system. I can go to msn and the internet, Checking my mail will do it also (sometimes) Mail providers (hotmail & bellsouth).

 

bbob - I'd love to try to help you out here but am real confused about what is going on. Maybe you could say the problem another way.

For instance, I have absolutely no idea what you meant by

 

Sorry. On second reading it is confusing. I partitioned my HD in half and loaded 2 systems. Then went to trouble shoot them. W98 was addressed previously (or most of it). Win2000 was even worse, upgraded to XP and I solved most problems, by going to microsoft and getting updates. My problem was and still is, but on a smaller scale, freezes or hanging-up to where I have to restart my computer. Morpheus almost doesn't run at all (XP side). I'm still in selective startup on both. Playing Windows mediaplayer is weird too. sounds garbled and lower volume than winamp (XP side). I think that it has to do with a program but can't isolate it or (really don't know how to troubleshoot properly). In answer to your ? I put in the disk for the mainboard on both my C & D drives. I do have some questions?
1) Do I need to do things to both sides, ex. IE6, morpheus,
2) What is NTFS? both sides are FAT32.
3) Can each side have different problems?

Maybe I should treat them as separates with separate problems. I made this investment hoping things would be better and faster, so far I'm not.