Did you find the solution or any workaround ? I've got the same behavior with mini PCIe DOM on the N2800MT and I don't know how to make it work !
Intel answer is that the DN2800MT cannot boot on PCIe because of the miniCard slot double compatibility miniPCIe/mSATA.
I think I have a similar problem: I installed a Kingston SSDNow MS100 32 GB mSATA drive, but the BIOS does not seem to recognize it. Do you have any hints?
May I know what it the brand and the model of the mini PCIe SSD that you are using?