Correct - the issue appears to be only related to this account for whatever reason. Nobody else has reported an issue on the server / I haven't been able to find anyone else.
We do have a per user php.ini setup, with the PHP_INI_SCAN_DIR setup.
Even a simple file such as you have recommend does absolutely nothing - it times right out.
I've tried ditching the php.ini and the .htaccess just to make sure there wasn't something dodgy in there but to no avail at all.