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There are some users who maintain that running hotfixes from an elevated command prompt is the best way to do it. (Which makes me ask - did you run from an ELEVATED prompt? You can't do it from a standard user account, unless that account is in the Administrator group.)
I will always run the hotfixes from within CFAdmin, unless my CFAdmin is hosed. This is especially important if you have moved your CFIDE to another location, outside of the webserver root. When the hotfixes are run from within CFAdmin, it is the CF instance that is performing the update, and it knows where all the files are located. When you execute a .jar from from a command prompt, unless you keep the default configuration, the .jar files assume the default locations and place the updated files, there.
If you have any way of rolling back what you did, and if you moved your CFIDE location to outside the webserver root, roll it back and perform the hotfix from within CFAdmin.
My my-server-name.profile document was corrupted causing a problem during installation. Using a corrected .profile resolved the issue.
#The following applies only to multi server scenarios.