So I have Windows 7 set up on my Mac mini and one day wanted had the need to boot into it after restart. I went to Startup Disk Preference Pane and noticed my Boot Camp device was no where to be seen. Deep breath. I restarted a few times thinking it was just a hicccup. No glory. Deep thought.. what changes did I make recently? Tuxera NTFS for Mac. 
A few days ago I needed to access an NTFS hard drive and be able to read/write to it and Tuxera was a timesaver. However I suspected that maybe it interfered with my Bootcamp device which proved to be correct. Tuxera automatically was “managing” my Boot Camp device so I had to go to Tuxera NTFS Preferences Pane and make sure that 3 check boxes were checked insuring that there would be no intereference.
Screenshot for reference only – does not show Boot Camp Device.
I then proceeded to do a restart and went to Startup Disk Preference Pane and Bam! My Boot Camp device is there!
All is well once again!