Odd, I cant reproduce it.
I installed the WPT, I am on Windows 7 64 bit.
I then ran my WMI repair, I watched as the repository was deleted and rebuilt and now a smaller size. I then rebooted and ran C:\Program Files (x86)\Windows Kits\8.0\Windows Performance Toolkit\WPRUI.exe
And I dont have any errors.
I wonder if the problem isnt that it needs to be int he WMI but maybe the WMI didnt rebuild properly from the last repair?
Backup this folder, just so you can compare file sizes after the repair again
"C:\Windows\System32\wbem\Repository"
Then run my WMI repair again and then you can compare the sizes, the new ones should be smaller since it gets rebuilt.
My WMI repair does the exact steps that Microsoft says to do on their support pages
Shane