OK you have ruled out a registry problem so you are left with either a IDE controller or software problem. The way I would proceed from here is to load up another HDD if you have one handy and see if the problem arises again. If it does on a minimum install of Windows you defiantly have a hardware problem of some sought.
Have you tried replacing the M'Board Battery? That could be going flat and causing problems and while I would expect to see different problems but I've seen enough strange things happen with a mostly flat battery not to rule out any possibility. If it is the IDE controller there is nothing you can do about it unless the M'Board is still covered by warranty in that case you can RMA it for replacement/repair.
But first if you do not have a spare HDD lying around I would buy one second hand and just load Windows onto it to see if anything happens like the problem that you currently have. If it works properly you know what you have to do and while it is painful it will most likely be your only recourse a reload of Windows, if that is the case the HDD will come in handy to backup your data to as you can not rely on the CD burner as a reliable destination drive to securely save your data to.
If a clean install of Windows doesn't cure the problem it has to be the M'Board as I seem to remember that you said that both the CD drives where on different channels and the only thing common to both IDE channels is the IDE controller.
While you could always use a PCI IDE card as a stop gap method if you need to reload the computer again the CD ROM will not be recognized for boot purposes so you will be stuck.
Have you cleaned out the case and Power supply as these things attract dust and crud like there is no tomorrow and there could be a problem in there but honestly it doesn't sound like a short caused by a build up of dust and other objects.