Unfortunately after compiling and testing with both Omega Ruby and X separately to avoid a conflict, it wouldn't auto-detect either of them. I also tested with Save Data Filer and that still works however. I'm wondering if it could be the filters on file size as Omega Ruby's main file is 472 KB (483,328 bytes) but clicking on the properties of the file mentions that its Size on Disk is 480 KB (491,520 bytes). X's file size is 405 KB (415,232 bytes) but its Size on Disk is 416 KB (425,984 bytes). I could be wrong however as I'm not sure if the file size filters were already there or not with Save Data Filer. Or for that matter if this is the actual problem.
I'm not sure on the most recent file saved timestamp as I don't know what that looks for.