Hi,
I have never seen this kind of situation, but I can suggest you to start debugging from CARD DETECT routine.
In linux kernel linux-2.6.35.3 CARD DETECT is done polling host controller, if you have the possibility to recompile kernel source you can try to bypass this check, to see when reset happens (file drivers/mmc/host/mxs-mmc.c) .
Maybe problems can be generated from power pin of MMC (file arch/arm/mach-mx28/device.c)
Do you see board reset also at u-boot level, if you insert SD in that moment ?
Giuseppe