Pykolab version is irrelevant here. What roundcubemail-plugins-kolab version? We had such an issue in the past, but it was hard to find the reason of it. I didn't hear about the issue recently, so maybe it's fixed or maybe not. To remove the tags you have to visit the Configuration folder and remove redundant objects. Do this in command line and then reconstruct the mailbox.

Kolab Plugins

$config['plugins'] = array(
         'kolab_auth',
         'acl',
         'archive',
         'calendar',
         'jqueryui',
         'kolab_activesync',
         'kolab_addressbook',
         'kolab_config',
         'kolab_delegation',
         'kolab_files',
         'kolab_folders',
         'kolab_notes',
         'kolab_tags',
         'managesieve',
         'newmail_notifier',
         'odfviewer',
         'password',
         'redundant_attachments',
         'tasklist',
         // contextmenu must be after kolab_addressbook (#444)
         'contextmenu',
     );

There are thousands of file in the Configuration Folder

Should I delete these and rebuild the folder using cyrus?

Thanks

I delete the config directory and rebuilt the mail box, every thing is back to normal.

This issue may be closed. If the bug reappears I will try to describe the process which created the situation.
Ed