I'm having the same issue on GRUB, also on a 2 IDE hard disc, after installing debian 8.2.0 (2015-09-09). The first IDE contains windows. As I've always done, I choose installing grub at the beginning of the second one, dedicated exclusively to linux (where installation was carried out). After installation is completed, the boot interrupts in grub file not found error message and the "grub rescue" interface.
This is all about the bug. Now follows what I've tried to do to overcome this situation, and failed solve it:
There I was able to verify that set prefix was mistakenly addressing to /grub, so correct to /boot/grub. But then I could not load any of the modules supposed to be invoked to start the boot procedure. Even though I could find the module files at /usr/lib/grub/i386-pc/, loading them results in "file not found".