What error message do you see in /usr/local/apache/logs/error_log when you notice the "500" error code in your browser? Have you ensured permission and ownership values meet the suPHP requirements?
I assumed it was a permissions thing, there are only 3 sites and one is working.
Initially googled and came up with 644 for files and 755 for folders, which didn't make any difference.
I've now spotted that the working site permissions are for the owwerwner, and the none working ones are for root:root, so i assume this has something to do with it. ?