I figured out what was going wrong.
When having what file it saved it as, I need to change it from Automatic to Flash, and just leave it at Flash 128k. Whoops should have figured that out earlier, now the files are working as they should. Yay for lots and lots AND lots of .savs! The crappiest part is going to be going through them all figuring out the SID. As I am wanting to do it on a Japanese rom, I'll have to do extra work in order for it to find the SID.
But thanks again to you and King_N for getting a working bot :)!