How to fix NTFS Internal permissions error in 10.8

I have a new Mid 2012 MacPro tower. I have one 3TB drive and one 2TB drive installed but formatted as NTFS. Reason for the formatting was to try to get them to work in Parellel as well.
I was running iTunes and Transmission at same time. iTunes on the 2TB and Transmission on the 3TB. Both programs locked up my tower. When I rebooted both drive show "Sharing and Permissions" to Read Only. When brought up in diskutitlity they both show Owner's Enabled to NO.
How do I get them back to Yes, so I can work with them?
I don't have an external enclosure to have windows fix them.

I was fine the drives for the past week. I do have MacFuse and Perian installed. Just when I had iTunes and Transmission up the programs crashed. When I force quit the system was slow and freezing. After force shutdown it changed the permissions on me to Read-only.
I tried adding a new user to the computer and logging in under it and still the drive is read-only. My video drive that has my movies on it I could turn back to MacOS after backing up the files with no issue if needed. But my iTunes drive (the 2TB drive) pulled my files from my old tower which was WinXp, so some of the folder were named same just with upper case here and lower case there. Makes it that the drive has to stay as NTFS.

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