I have seen the same, though on a smaller scale. Upgrading to Agent 5.0.4 has resolved several of our issues.
You may want to look into upgrading to VSE/HIPS Patch 8 and see if that resolves any of your issues, also.
There is a policy setting, IIRC under the Access Protection, which 'prevents McAfee Services from being terminated'.
I would suggest checking this be a first step.