I have not seen this before but I would recommend using procmon to see if you can spot exactly what is unregistering the .dlls in question. You should be able to filter the results on the .dll name to quickly spot what is going on.
Were you able to determine if Mcafee Agent update had caused this?
We are facing a similar issue where we are finding vbscript.dll unregistred on a lot of PC's after doing a upgrate to Virusscan 8.8 followed by a Hotfix update through ePO.
After a little investigation, it seems effectivelly it is not caused by the mcafee Agent but by mcafee Viruscan 8.8 itself (followed by a hotfix update).
now, i don't know more about this. so, we are two with the same case. A bug in the viruscan install or in the hotfix ?
I am also experiencing the same issue you guys are seeing. I am seeing these issues come up not after the VSE 8.8 install, but it appears to be related to the VSE 8.8 Patch 1 upgrade that triggers it.
Did anyone get a resolution for this? I am having a similar issue.