Question about Use of System Restore

I have had a series of spyware infested machines referred to me. I refer to Wilders for assistance and read thru the threads for information to remove the infected files and registry entries.

My question centers around when to turn off System Restore and when to turn it back on.

It seems to me that we should turn off System Restore at the beginning of registry changes (using Ad-aware, Spybot, CW Shredder, and especially HiJackThis). When all is cleaned out, we should turn System Restore on again.

My thinking is this: If the malware entries are still in the saved registry (not turned off) then they are still protected (and able to reactivate?) in some form. If System Restore is turned off, then the aforementioned spyware removal programs can delete them from the registry.

If my thinking is correct, then why is System Restore never mentioned by the moderators. Of course, my thinking is probably wrong, so please set me straight. Thanks in advance.