I’ve run into this twice in as many weeks, on Windows 2008 when running the ColdFusion 9.0.1 updater it will fail to complete successfully.  Each time failing with the same message in the install log:

ANT Script Error:
Status: ERROR
Additional Notes: ERROR - cfmx-patch-move-files-all.xmlFailed to copy C:ColdFusion9libcfperfmon_9.dll to C:Windowssystem32cfperfmon_9.dll due to C:Windowssystem32cfperfmon_9.dll (The process cannot access the file because it is being used by another process)

 
Each time, however, I was able to simply rename the dll while ColdFusion was stopped and the upgrade continues successfully.

Recently did an upgrade to ColdFusion 9 from ColdFusion 8 for a customer and ran into an issue with ColdFusion failing to restart after I was done importing the .car file I had created.   In the coldfusion-out.log file I was seeing the following entry:

Error: no known VMs. (check for corrupt jvm.cfg file)

Checking out the jvm.config file, I realized that I’d imported the old JVM path that referenced ColdFusion 8 (and no longer existed), updating to the ColdFusion 9 path allowed ColdFusion to start correctly.