That's a bit unusual, as I've dumped a few SNES and GB protos that are different from final with the Retrode (2), without any problem. Not saying it's perfect, it is hit-and-miss. I think I read a post somewhere on the retrode forum addressing this, but am not sure.
I don't know about sms, but I can suggest some alternatives for GB and SNES, if they'll interest you somewhere down the line.
BennVenn; for GB, GBC and GBA; available here:
http://bennvenn.myshopify.com/...
Altane; for GB and GBC, however, it's not in stock last I checked
Mash-Mods; for SNES, as stated above (highly recommended); need to email the person