Hello Cheng,
I am afraid, I have no ideas anymore what could be wrong. But I have for you one suggestion (path to resolution, maybe).
No idea what you are using. In the sense BYT-FSP (MR5) -> Coreboot -> (payload???). You either use SeaBIOS (CSM ON), or Tiano Core/EK2 (CSM OFF).
I would suggest the following: since it depends what payload you use because you would like to reuse your old HDD with WIN 8.1, to make test very short (no need to install other HDD with WIN 8.1).
Please, take real UEFI BIOS (for BYT-M N2807 it is Client Group 64bit A093.R42 or later), and install it on some INTEL CRB (BayleyBay or BakerSport) where you already have N2807. Then, in relations what payload you are using, you need to set CSM ON or CSM OFF, to make work/reuse your original HDD with WIN 8.1.
Please, after you are able to bring your INTEL BYT-M CRB to WIN 8.1, reboot, and again enter BIOS CMOS. There, under system setup/advanced settings, you should be able to find southbridge setup, where one of the options is LPSS.
Please, experiment, with settings within LPSS mode (PCI and ACPI), and, please, report here do you have the same as with BYT-FSP MR5 settings as you use "pcdlpsssioenablepcimode" to "LPSS_PCI_MODE_DISABLE" and "ENABLE/DEFAULT" (do you see the same behavior in WIN 8.1 device manager)?
Thank you,
Zoran