re-name them all with .sav as the ending and they'll be good to go.
Google "Defraggler" download it and run your saves through it. People swear by this program.
:/...why are you suggesting things that I have only heard WoodR4 users ever need to do...
OP: Did your save files still work with the older firmware? Actually come to think of it, why do you even need your old saves if you aren't even really playing the games anyways xD? Anyways, possibly try converting a sav file using shunyweb to the R4/TTDS/etc. type (kind of only going to work if your flashcart is like...really old probably).