Maybe you want to try this "fix". I had to do this on my brothers PC. He had Windows XP SP3 up and running, and he wanted a seperate harddrive with Windows 7 x64. Instead of making a bootselector or use the bootselector in motherboard, you can try and go into BIOS. Set the harddisk you want to install Win 7 x64 on as FIRST HD BOOT choise (you can still have CD-boot selected before HD's, if you prefer), then boot install DVD, install on the first HD (this will be the one you use for x64). If it can install this way, then a BIOS-update might fix the problem, or you can just go on using your x64 this way.
Then use your mobo's bootselector to choose which system you want to boot, instead of having Windows to make boot-selections. In this way you can allways delete one of the systems without the other to refuse to boot because of missing MBR.