I had a similar issue with PiSnes where it just wouldn't save. I finally tracked it down to file permissions. The write was being blocked but I couldn't find any logs or any information to indicate it. chmod 777 on the srm file and I think it's working fine now.

Edit 1: I just did a quick test and new save games are being created without proper permissions so after the first autosave, or save after quitting it will fail to continue saving.

Edit 2: In my case it's because I mounted my games on a network share and the samba configuration wasn't right. Following this did the trick:
http://askubuntu.com/questions/97669/i-cant-get-samba-to-set-proper-permissions-on-created-directories