If whatever was wrong before was caused by software or malware, you have eliminated that if you re-installed Windows.
However, if you ran a Repair Setup instead, the problem may still be there, because a Repair Setup can't fix problems caused by anything that isn't on the Windows CD (CDs in this case, if it's an OEM copy of MCE).
Whenever you install Windows from scratch, after Setup is finished you must load the drivers for the mboard, particularly the main chipset drivers, so that Windows has all the proper drivers for and information about your mboard.
E.g. If you don't do that it's quite common for the drive controllers to not be detected correctly, and the hard drives and optical drives won't run as fast as they are able to.
If they are IDE connected, all your hard drives must be connected to 80 wire IDE cables in order to run at their full speed. If you have a DVD drive that is capable of DVD +R or -R 16X or greater it must be connected to an 80 wire data cable if it is IDE connected in order to run at it's full speed.
Check your hard drive with the manufacturer's diagnostics.
See the latter part of response 1 in this:
http://www.computing.net/windows95/...
If you don't have a floppy drive, you can get a CD image diagnostic utility from most hard drive manufacturer's web sites, but obviously you would need to make a burned CD, preferably a CD-R for best compatibilty, on another computer if you need to.
A common thing that can happen with ram that worked fine previously is the ram has developed a poor connection in it's slot(s).
I've had even new modules that needed to have their contacts cleaned.
See response 2 in this - try cleaning the contacts on the ram modules, and making sure the modules are properly seated:
http://www.computing.net/hardware/w...
If this is a laptop, you must remove both its main battery and AC adapter before you do that.