Ho ho. As soon as I post my satisfaction here, I get the funky 'R4 not recognized by DS' problem. It appeared while playing Lunar Knights. I'm beating on zombies and suddenly the game tells me I removed the card and to turn off the system. When booting up, the card was not recognized. I reinserted the microsd and the R4 back into the DS and haven't had the problem since then. Been doing a lot of Meteos lately. Good stuff.
i had that problem exactly once just like yourself the second time i turned the thing on. i took it out, pressed the casing together some to make sure it was closed tightly, reinserted and everything has worked flawlessly to this day. I LOVE MY R4 to death and have no regrets.