Whenever the file-based repository gets corrupted you have to shut down IS, delete all the files from WmRepository2 but before you reboot set the following property in the %wm_install_dir%\WmTN\config\properties file: tn.webmgr.60config=false. This will tell IS to not look for permissions in the repository when it boots up.
TN stores your permission configuration for TNWeb in the repository so when it gets corrupted or deleted you lose this info.
#webMethods#B2B-Integration#Integration-Server-and-ESB