Both my desktop & laptop have identical programmes including Spybot which is the same version on both.
On my laptop the scan usually takes about 40 mins and on my desktop about an hour.
The last two scans on my desktop have taken over five hours each time whereas the laptop continues at 40 mins.
I never have anything running in addition whilst the scan is performed.
I have used Spybot for many years and have never encountered this problem before.