The name of the file have nothing to do with the R4 saves not working. The R4 handles saves differently. Also, the setting there is for personal choice. Some people want the .nds in the file name of the save so they know what goes to what.
Not much, some people suggest using a piece of paper to make sure the cart is fully making contact with the ds. I'd try the paper first, then the tape.
Did you flash the card to support DSi's with the version 1.4? Also, was there any thing you did around the time that it started to get worse?
Just trying to figure out whats going on
Yep, if it was flashing it and you turned it off/pulled it out its bricked. You might be able to start the DSL patcher from your card and reflashing the broken one.
Hmm. Looks like the right one. What about putting a different microSD card in the problem acekard? I'm really lost on what to do, other than to get it replaced.