You can fix this either with command-line tool bootrec (not really user-friendly, but no 3rd party software required) or with EasyBCD (GUI-based, user-friendly). If the other one still doesn't know about first one, then switch master drive, boot the other OS and repeat. Try it on first drive, then try rebooting to both systems. You will probably have to apply the fix to both drives. That makes drive bootable independently from other ones, but also creates this problem: you have two boot configurations that have to be managed separately.
when you're installing Windows with other hard disks disconnected.
I suspect that your Windows installations are unaware of each other - you have bootloaders and EFI partitions installed on both drives.
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