./bin/shell/clearcache.sh --clear-all
Removing sortkey cache files in var/cache/sortkey_
Removing class identifier cache files in var/cache/classidentifiers_
Removing class attribute identifier cache files in var/cache/classattributeidentifiers_
You can see from the output that not all the cache is cleared. The clear all cache function in the admin panel works perfect.
There is already bug report about this issue.
Have you tried patch submitted in this bug report? http://issues.ez.no/IssueView.php?Id=9890&activeItem=1