2nd disk causes boot to fail

I installed Windows 7 64 bit to replace Vista 32 bit. I have 2 physical disks and did the install with both disks installed. Now when I remove the 2nd disk it boots fine but won't boot with the 2nd disk installed.

My first disk has 2 partitions: c: (where vista was installed) and d: for everything else. When I boot from the installation disk to do a repair, the os field is blank. When I use bootsect.exe it only offers d:

I have read plenty of examples win this forum and others for replacing the mbr but none have worked. I also tried formatting the 2nd drive but that didn't work either.

I just want to use the 2nd drive without the system files as a backup. What can I do?

Does this help?

Many thanks Bare Foot Kid. I had actually tried that before but I did it again. No change except that the os appears correctly in c: during the repair.

When I install the 2nd HDD and reboot it boots straight to the ODD. I checked the BIOS and the boot order shows the 2nd drive correctly as third. When I look at the disk mgmt the 2nd HDD is not shown as system but there is a locked system information folder in it in explorer.

Why is your C HD showing as both DISK0 and DISK1 in screenshot? Are you using RAID0? Which port is plugged into if single HD is used?

As the M:Backup drive seems to be causing the problem and is empty according to DMgmt, I would delete, create new and format it in Disk Mgmt.

If this doesn't solve the problem, try plugging Win7 HD into different SATA port to see how it registers. Be sure to set it as first HD to boot in BIOS setup.

Disk1 is an SD card reader.

I tried to delete the system folder in M:Backup but it won't let me. I tried giving myself full permission but still couldn't do it (I may have got this wrong of course).

You suggest I put the 2nd drive in first - I haven't tried that as I wouldn't expect it to boot. Wouldn't it just repair into the main os?

Wipe your M drive using DISKPART from elevated CMD prompt: Clean and Clean All with Diskpart Command

If you move your Win7 HD to another port, you'll need to change it to boot first in BIOS setup.

Thanks, that seems to have made progress. However, the cleaned disk does not give me the option to format or partition. Did I do something wrong?

OK thanks to your advice I managed to get the disk initialized with 2 partitions as you suggest.

However, when I reboot I get the same result - straight to the DVD. When it goes through the repair procedure the OS is blank. I can still only boot without the 2nd HDD.