As occasionally happens, the url rewrite function gets stuck. You can’t refresh it, because it says it’s still processing.
This can happen when it finds a duplicate record in the database and then throws an exception. This stops the url reindexing dead in its tracks.
If you turn on logging, you will be able to find the exception and will have some clues as to what’s going on.
If it is due to a error when writing urls, you should be able to manually flush out the rows in the core_url_rewrite table and have Magnento rebuild that index. First, make sure you do a full backup before doing anything with the database ( use a SQL dump, not a Magento backend as these have been known to be faulty). Make sure you get everything out of that table, because it can have a lot of rows (10K+). Now go back into admin and refresh the url rewrite index, and everything should be fine.
Good luck.