Can you share the link where this is happening? (PM if you do not want to make it public)
Never mind, I found the problem.
The form module, since WB2.8.2, suddenly uses the $_SERVER['SCRIPT_NAME'] variable as the url to post the data.
The script_name is the script that is used after rewrites. This means it will use the /short.php for posting the data.
Previous versions of the form module were using $_SERVER['PHP_SELF']. That will show the original request before any rewriting.
The good solution would be to modify the form module (view.php) and modify all 'SCRIPT_NAME'
The dirty solution is to modify /short.php and add before line 40 ( require.... ) a line that says: $_SERVER['SCRIPT_NAME'] = $_SERVER['PHP_SELF'];
This will fake the correct value in the SCRIPT_NAME variable..
Note: This could break (or fix as well) other modules that make use of that variable!