I can think of a few possible causes. Try creating a simple test.php file in the subdirectory in question, like this:
Code:
Text Test
<?php="PHP Test" ?>
Start by accessing the test file directly. If you don't get the PHP Test text when accessing the file directly, the problem is with executing php in the subdirectory; if you don't get any text at all, the problem is with the server dealing with files in the subdirectory (permissions maybe).
If everything works when accessing the file directly, check the SSI. If you get the PHP Test portion, the problem is with the script you were trying to use, some ini configuration setting has changed and broken the script, possibly a change in how some environmental variable is handled. If you only get the Text Test, the problem is probably in the PHP.ini file, and the resolution will depend on how your server interacts with the PHP interpreter. If you don't get anything with the SSI, it is a problem with the way your server handles subdirectories... check if there is or should be a leading slash, and check the config.
Unfortunately cant really tell you anything specific, but this should help you narrow down the source of the problem.