[Jon]

Has clean urls been removed from your .htaccess entirely?

I don't know what the problem with that would be off hand. You could try opening init.php and finding:

x_load(
    'db',
    'files',
    'compat',
    'gd',
    'clean_urls',
    'memcache'
);

And changing to:

x_load(
    'db',
    'files',
    'compat',
    'gd',
    'memcache'
);

But I'm not sure if that would simply cause function does not exist errors.