I'm using a previous install of ME (not a fresh install). I, too, was thinking that I need to try a fresh install of Windows, however, I did successfully 'migrated' Win98 to a new MB in this same fashion (you just have to remove all of the device drivers from within Device Manager and do a 'refresh' and load the new drivers).
I made a Ghost backup of my C drive in preparation to delete Windows and try a fresh install. I haven't had a chance to delete and re-install, yet.
Another strange thing, and possible the 'real' problem, is that I get an (false) virus warning when in DOS mode booting with EZ-BIOS (or some name like that). If I boot straight form the floppy, DOS boots fine without any virus warning, the only problem is that my D: partition shows up as C: and I don't have my original C: partition. If I start to boot from the HD and wait for the EZ-BIOS to load, and tell it that I want to boot from the floppy disk, I get a virus warning (which I didn't get without the EZ-BIOS). If I tell it to continue anyway then all seems fine in DOS--I can when see both the C: and D: partitions (this is what I had to do for Ghost to see the C: drive).
In Windows, I sometimes get this same virus warning during start up, but the DOS box won't let me continue, in fact it doesn't seem to take any keyboard input and basically locks up (although the mouse and num-lock key still work). So I wonder if the problem is from some weird combination with MB's Trend Micro anti-virus software (which is a boot virus detector running from BIOS) and the EZ-BIOS (prevously installed) on my HD????
I think that I'll try either disabling my BIOS anti-virus software, or removing the EZ-BIOS from the HD (however, I don't know if that latter is possible).
My final attempt will be to try installing Windows XP and see what happens with it. I was planning on eventually using this PC as a second computer, so I didn't want to install XP if I didn't have to.