there is a deeper format, needs boot from floppy or cd. You may find vistas option does something a bit too quick to make much sense. In this case, have a registry cleaner, defrag software available when it does get into the first run of its so called "clean install".
It has been a backfiring peeve of mine on high hours computers...for about a decade now..
wd hard drive? they have software from boot that REALLY sets it up clean and even tests it, with a dated logfile recorded.
if you are repairing serious error, completely new hardware, or big change like vid card. go for deeper slow format, partition. Use your bios memory tester, just for the sake of cleaning it out, clear ram.
the least of the problem the quick clean is the acpi does not stay smooth. in other words, all is working, but power stays a bit more than it shouldn't..there is a ghost that needs exorcism.