Almost forgot...
along with what I posted above, Zero write is the only way he will kill it. The Windows repair will not work because he has no Windows install on the 2nd drive. He needs to get the data off that drive and wipe them both AGAIN (ENTIRE DRIVE NOT PARTITIONS) and then start clean
Have him check his BIOS and make sure the Windows drive is the one set to boot. He can even REMOVE drive 2 and see if that makes it go away. If it does, the loader is hidden on the 2nd drive.
Unless he has some type of wierd virus or bug that is infecting his boot sector, thats all I can think of. A FULL zero write to both drives should squash it unless its hidden in his data somewhere.
However, I suspect this is just a matter of the 2nd drive has the boot loader and nothing else, and somehow the 2nd drive is getting enabled in the BIOS (bad battery?)