Hmm. If I'm reading the manuals correctly, SD_B0_05 (J2) is supposed to be DAT3, not DAT2 and SD_B0_04 (H2) is supposed to be DAT2, not DAT3. So something does appear to be swapped. If the labelling on the chip side of things is correct then yes, the DAT2 and DAT3 lines at the SDIO pads would appear to be swapped. But how on earth would the a uSD card hooked up to the SDIO lines even work then?
Maybe if data written if swapped then read if swapped is the same. But commands? Curious...
Commands were what I was thinking of too; swapped data lines you likely wouldn't notice until you took the uSD card out and plugged it into something else. But commands shouldn't work at all if they make use of all 4 lines and the 2 lines were swapped. Someone would have noticed months ago. I wonder if it's just the labels on the IC side of things that are swapped on those 2 lines?