Something is eating up process time or you are having big time memory problems is all I can think of right now.
Did you run Kaspersky *TDSSKiller* free and stand alone to make sure you didn't have any *rootkit* type of virus messing with the registry, these are very nasty.
For me (around2003) a Malwarebytes scan is about 3 hours.
Superantispyware is a little over 4 hours.
The processor on here is listed as AMD Athlon (tm) II P-320 Dual Core. Memory is shown as 241gb free out of 286gb. Other than their usual anti-virus, I don’t recall having run the TDSS Killer. I can try running that when this is done, but I have no idea how long this program is going to take (now at 2hrs, 45min — and still showing no objects detected).