I was having trouble getting short URLs to work for my conference. I tried every solution I could find on these support forums and ended up going in circles.
It turned out that with our hosts combination of Linux, Apache and PHP that when mod rewrite is used the values that would normally be in PATH_INFO were now in ORIG_PATH_INFO. Instead of modifying the 4 or 5 references to PATH_INFO with a straight find and replace I followed the advice found at http://infopotato.com/blog/index/path_info
and made each instance test for both. I ended up having to take a slightly different approach for each instance as some test for a value and then use it, others test for the value not existing, etc. While I would be willing to share my code I would suggest that a better approach would be to take the PATH_INFO or ORIG_PATH_INFO value and put it into an OCS constant and then change the references to use the constant. This would also enable the possibility of cleanly dealing with the IIS issue mentioned at the blog.
I would guess that OJS would have the same problem.