I have the same symptom but both the system32 version and the dllcache versions for those files are 5.1.2600.3093 so I'm not sure that's the file that is getting replaced. I did notice that the version in system32 has an extra underscore in the name so perhaps it is the issue.
I have repeatedly reported the problem to Parallels support, but the responses I got showed they either didn't even read the support ticket or they are completely ignorant of stuff that anybody doing tech support for windows related things should know. I got great replies such as
"Please go to Configuration Editor -> CD/DVD-ROM -> check Use CD/DVD-ROM
Drive if it isn't checked -> OK -> start Windows -> maybe it will help. "
"It is well-know problem with activation some software on VM from Boot
Camp partition.
We working hard on it, but now we only advise to address to company you
purchased software and explain, that you use the same computer with it. "
and finally
"Please explain me what is KB890859?"
I finally gave up. If someone figures out what is going on and a solution, I'd love to hear it. Right now I either deal with the long shutdown time while it applies the patch, or the next time I boot it applies the patch anyways and then forces a reboot.