Eek, this is happening to me too now (but the original Pokemon White still works..).
I'd format my SD, but since the USB micro SD reader that came with the Acekard broke (didn't last more than 3 weeks), I have to use an SD reader on my wii with the WiiXplorer to transfer stuff from a USB.
Does anyone have the slightest idea on why this is happening?
Same thing happened to me, but I never got a chance to play Pokemon Black or White. In fact, I rarely every played it after I got my DS TWO. Just one day, when AK team releases a firmware update, I try to get it to run, but the flash cart doesn't run one bit. Paper trick doesn't work, and the updater doesn't see the card even after I run it from another card on my ds lite.
I don't think it's any particular version, I think I was using 1.7 something and I unbricked using tk_saturn's first suggestion, then I got the latest (1.8.1, I think) and it was still a problem.
Oh and the unpatched one worked perfectly.