I've been reading over at Reduser and this is a problem that multiple people are having. Some people have said that it is related to the Red files with audio (which mine do have). its to bad its main point is for refrence.
Yes, this is a known bug that we're working on. It only affects R3D files with multiple audio tracks.
I actually found a way to work around it. I simply made a new sequence but one that was 24fps instead of 23.97.
The Red footage was shot in 23.97, but I tried interpreting the footage to 24fps and the timecode corrected itself or at least matched the slate it was jammed too). So then I created a new 24fps sequence (if you drag 24fps footage into a 23.97 sequence it will play it back at 23.97).
It seems like Premiere thinks the Red footage was shot in 24fps instead of what it actually was shot at (23.97)
Anyway, that was my solution... for the time being.
stick your 23.97 footage into a 24fps sequence
This is still an ongoing issue. It does seem that PPro correctly reads the 23.976 TC if you incorrectly interpret the footage as 24 fps. I have to say that I've had ongoing issues with bad TC handling in PPro since CS4 (I never used an earlier version of PPro.) It makes it VERY hard to collaborate with other facilities. Is there any progress on this?