I've noted that the Disk Clean option in Utilities doesn't get rid of absolutely everything and have occasionally run the Windows equivalent.
I did so today and found it was very slow, seemingly getting stuck on "compressing old files". I looked for and found a fix for this, involving REGEDIT. There's a suggestion that when the problem occurs, it's because Windows is looking in the wrong place for the approprite registry entry. Is there any chance this could be affected by the Registry Clean option in Utilities?