Big news update on this issue :
I reworked all the download code on both the ROMS and EMULATORS database and as a result (and with thanks to rckclmbr for pointing me in the right direction) all roms can be downloaded in any browser, comma or other characters will not effect the download.
Its all working again. This was a great post and actually led to a needed fixon the website. For everyone involved I just want to say thanks.