As suspected because you kept the old OS HD plugged in during install, the new install put its boot files (System Active) on the old partition.
To correct this, mark the new Windows 7 partition Active, then mark the old Windows 7 partition Inactive using Diskpart from this tutorial: Partition - Mark as Active
Power Down to Disconnect the old Windows 7 HD to make sure it doesn't interfere, swap its cable to new Windows 7 HD or set it as first HD to boot in BIOS setup (after DVD drive). Boot the Windows 7 DVD Repair console or Repair CD, accept any offered Repair, when it doesn't restart boot back into DVD Repair, click through to Recovery Tools list to run Startup Repair up to 3 separate times with reboots to write the System MBR to Windows 7: Startup Repair - Run 3 Separate Times
After the new Windows 7 starts up, again power down to plug back in the old Windows 7 HD to clean it using Diskpart then repartition in Disk Mgmt: Disk - Clean and Clean All with Diskpart Command
If you'd prefer to have a graphical interface rather than using Diskpart to mark Active/Inactive, wipe the old HD and repartition, use free Partition Wizard bootable CD: Free Download Magic Partition Manager Software - Partition Wizard Online