There's tons of things that can cause this. Here's some examples:
1) System restore turned on in the guest - the system restore is off in the VM
2) hybrid disk drives (see other thread)??
3) Antivirus software doing scheduled scans - not seeing any scheduled scans and my Mac has the VM excluded
4) Failing hard drives - not seeing it outside the VM
5) starving the host for RAM or CPU ??
6) Time machine (make sure that you've excluded the VM from backups - they don't work anyway, and it'll cause this problem). time machine is currently off
7) Missing or out of date VMWare tools. no updates available for my current version
and others as well.
If you're on 10.8, Fusion 5 has better support.
My mac is only at 10.6.8... we are not currently upgrading the OS anytime soon...