I highly recommend that you install that new motherboard and new hard drive in the PC and install Windows clean on it. The boot manager could be just the start of the problems.
If you installed Windows on the new drive connected to the old motherboard then all of the drivers are for the old motherboard. You might have to perform a Repair Install to get the correct motherboard drivers installed to use the new motherboard. Even then you will have old drivers and phantom devices in your system. Messy, not clean, which could lead to odd problems in some cases.