The system that I'm looking at is Windows 7, 32bit.
When the system boots up it spends a ton of time reading and writing to the DataStore.edb file which is located in Windows\SoftwareDistribution\DataStore directory. This makes the system run really slow for several minutes, probably about 10 if I'm honest. If you stop the Windows Update service, within a minute the system will stop reading and writing from the file and everything runs smoothly.
Things I've tried:
I've stopped Windows Update, deleted the file, rebooted, but when I do that Windows rebuilds the file until it's a few hundred MB in size. Once Windows is happy with whatever it's doing, it stops and my disk usage and cue drop down to normal levels and the system does whatever you want with plenty of speed.
I've booted into SafeMode and run several virus scans and Kaspersky's RootKit killer tool and nobody finds anything offensive.
What should I try next?