I too have purchased a mSATA drive to do this, and straight install of W7 on the mSATA doesn't let the device boot (not without the W7 install DVD present). It boots fine from the mSATA when the w7 install DVD is present. So it looks like I'm missing the boot loader. Can't get the system BIOS to recognize the mSATA drive to be able to boot from it - so the system can't access the bootloader on the mSATA drive.
BIOS settings are as you describe above.
So I guess what you're doing with the double install of windows (on the mSATA and HDD) and then using EasyBCD, is re-pointing the bootloader on the HDD system partition (the small hidden one) to point to the mSATA install. So you've set-up a bootloader on the HDD system partition, which can be configured as bootable in the BIOS, and then re-directed the actual boot to the mSATA drive.
Looks like I'm going to need to by a new HDD too! Looks like your the only person who has managed to get this system to actually reliably work using a mSATA as the boot drive.
I'll let you know who it goes.