Sorry for bad english.
Error bootfile Windows version, if it launches image on non-priority drive

I have two hard drives. First hard drive Samsung HD0, the second Western DIGITAL HD1.
Windows loaded from the first hard drive Samsung HD0, that is, the loader bootmgr on HD0. Kernel Windows 7 on Western DIGITAL HD1.
If I run a bootfile to launch IFD of Western DIGITAL HD1, get lost MBR partition table on the disk Western DIGITAL HD1. Because the priority HDD in the BIOS - Samsung.
How to beat this bug?
Is it possible to use script Windows version TBOSDTS for determining the priority HDD in BIOS and validation correct run bootfile on priority HDD? How

Use script diskpart sel disk=system possible, but not desirable ...
Thank you.