I have been having this very weird problem with Diskeeper 2008 Pro, running on my X61 with Vista Business x64 SP1 installed. It can analyze and defragment external drives with no problem. But whenever I try to analyze or defragment the boot drive [c:], it breaks. It doesn't crash or BSOD. But the analysis terminates prematurely, and the defragmentation job report shows ridiculous discrepancies. For example, the summary will say average fragments per file is 1.01, but the warning section will say the disk is in critical condition because the average fragment per file is 4 million

, and that disk free space is zero. Well, my 7K200 is not even halfway full...
I switched back to the Windows built-in defrag, and running it from the command line gives me good feedback on how it is actually doing its job.
Anyone experience similar problems? I called Diskeeper support and the issue has been elevated from vanilla customer support, to dedicated tech support, to now developers. I am still not sure if it's Diskeeper's fault or the OS, because when I tried Diskeeper 2007 trial version, it exhibited the same problem.