Time Machine keeps excluding my hard drive I have Time Machine set up on a FireWire 800 external drive on my MacBook Pro. I have another USB external drive (formated NTFS with Paragon drivers so that I can store files bigger than 4 GB and access them from Windows) with  iMovie media etc and TM has been backing that up successfully (I can see the files in TM disk).

Recently I ran out of my internal SDD space and moved iPhoto Library to that external USB drive.
Then I got fed up with constantly connecting the USB cable and decided to swap HDD and optical drive (using a solution similar to OptiBay). Again, everything is working fine.

The Problem is that I discovered that Time Machine has not made backups of the Media disk in a while (backups don't contain the iPhoto Library).
Turns out that TM has that disk in the exclude list for some reason.

No matter what I try, TM keeps adding the Media disk back to the exclude list every time I open the Options... from TM prefs.

Some details:

Mac OS X 10.7.3

The disk in question is split in two partitions:
  Media disk: NTFS, 400 GB with 290 GB used
              I can remove it from exclude list, but it reappears
  Stuff disk: FAT32 - never needed to be backed up nor ever has been
              grayed out in exclude list, can't even remove
TM disk free: ~ 500 GB
Latest backup of Media seems to be March 2, 2012 (TM browser indicates),
  which was prior to moving iPhoto Library


BTW, now that the disk is internal anyhow, I can reformat the NTFS partition to HFS+ if that solves the problem. But TM did not have any problems with NTFS in the past. Why now?
Why it was possible is strange in the first place. The change may caused by a decision of Apple, packed in an update.

Reformat the NTFS partition to HFS+, will include your drive in Time Machine.

Note: also FAT formatted drives will not be backed up by Time Machine.

Update: Time Machine offers to use an NTFS volume if a write-enabled driver for NTFS is installed before a physical disk with NTFS is introduced to OS X. [source: Enabling Time Machine for a USB HDD with NTFS