UBB.threads is a web script; our support is geared towards our own script operating on a standard web server that we assume is operating properly (we test it to do so with every new release of PHP and MySQL). System web server configurations are out of the scope of user to user support as we always assume your web server is in working order (problems with your hosting environment are issues your host should be managing). The test script and control panel notices are designed to inform you of potential problems with your environment (max_input_vars for example can wipe your UBB.threads configuration file in some rare circumstances, because all of the variables cannot be passed to the back-end systems if the value is too low).
This forum is also a user to user support forum (the vendor, UBBSystems, does not regularly view this forum (as member support is obtained through the member system).
That being said, here are some links from Google:
MultiPHP INI EditorPHP.INI.USER.INI (suPHP)
Managing your max_input_vars you could try manually editing the existing php.ini and inserting the values, or asking BlueHost to manage them for you (while indicating that the system editor is causing instability in your web script).
The MultiPHP manager is a part of the cPanel Webhosting Control Panel, docs can be found
here.