Hi. I'm a noob but I think I had a similar problem.
Legacy BIOS on laptop with 2 identical SATA disks.
Windows 7 on /dev/sda1. Installed jessie 8.7.1 from USB on /dev/sdb2 (swap on sdb1)
Grub wanted to install to /dev/sda MBR but I wanted to keep the windows installation native and boot Debian from /dev/sdb using BIOS boot options. So I specified /dev/sdb MBR as target for grub.
Completed without error but then not bootable from /dev/sdb. Once it said "Missing operating system" but mostly there was just a blinking cursor
Installed without errors and now working as desired.
I'm happy to provide any logs that would help but might need some guidance to find the relevant info.
David