Windows 7: Partition is "Active" and "System" though it shouldn't be

Hello everybody. Here's my story. I have 2 HDDs:
1) 1TB with 2 partitions: System (where Windows 7 is installed) and Hard Disk (with programs)
2) 500GB with 1 partition: Storage (with all the unnecessary files I don't want to delete)

My problem is that the last partition became Active and System. It happened like that. I had some troubles with SATA cable so I had to disconnect my main HDD and connect DVD-Drive with that same cable and my main HDD with the one I used for DVD-Drive. What I didn't notive at first was that the 500GB hard disk became the first one in the boot row. After some time I noticed that Storage became my Active and System partition. I tried making the partition with Windows Active and making that one Inactive but I couldn't load the system after that, I had BOOTMGR is missing error, so I had to swich back with Paragon software. Any ideas how can I make my original System partition to be active and system and that useless partition to become simple data storage once again?

Plug 1tb into first SATA port, mark it Active using Diskpart from Windows 7 DVD Repair Conosle or Repair CD, or use free Partition Wizard bootable CD. Then mark Inactive 500gb plugged into Disk1.
DISKPART At PC Startup
Partition - Mark as Active (Method Two)

Set 1tb on DISK0 as first HD to boot in BIOS setup, after DVD/CD drive.

Boot the Windows 7 DVD Repair console or Repair CD to Startup Repair - Run 3 Separate Times until Windows 7 starts on its own and is correctly marked System Active. You may have to unplug the 500mb HD if it interferes.

Thanks a lot, that helped.