There seems to be a workflow kink am not able to replicate with any other media but it is right now a bane of my existence.
A client gave me a 27m long Cineform.AVI file that they rendered out of their NLE (on PC) flat using free version of Cineform codec. When I open it in any video app it reads as 23.976 fps file.
I then convert it into a Cineform.MOV via HDLink (on PC) it becomes a 23.980fps file. At first I thought it was just a shorthand for 23.976 (ie fcp 23.98 is actually 23.976) but all of the apps both frame based and stream based report 23.980.
This causes me a lot of grief trying to conform the footage for a grading session.

I was not able to replicate it with any footage I have, although I obviously have a full version of the codec, and I haven't tried it with any of the clips that are that long.

Another problem: when I am trying to trans-code the client's .AVI using adobe media encoder (CS6) into .MOV file using the Quicktime routine (Cineform.MOV routine seems to not output anything above 8bit so it is unusable) the render fails with the log file showing the render has failed with non specific error message.
Any thoughts?

The footage is still 23.976, many tools report 23.98 and they are wrong, there are complex reason for this. This is nothing to do with the codec, just the frame rate in the header of the MOV. Some applications (if confused) you can interpret the the footage to the frame rate you need.

The CineForm QuickTime export has been fixed, that fix in the last or the next buid (support can get you a build it isn't released yet.) PPro's QuickTime I/O does seem to be 8-bit, yet AE is 16-bit and works fine.

The footage is still 23.976, many tools report 23.98 and they are wrong, there are complex reason for this.

To elaborate on the complex reasons. The frame rate is actually

24000/1001 = 23.97602397602397602397...

which as you can see is some sort of repeating decimal. When most video applications see a frame rate close to 23.976, they understand the user really meant 24000/1001 and use the exact value accordingly.

The footage is still 23.976, many tools report 23.98 and they are wrong, there are complex reason for this. This is nothing to do with the codec, just the frame rate in the header of the MOV. Some applications (if confused) you can interpret the the footage to the frame rate you need.

The CineForm QuickTime export has been fixed, that fix in the last or the next buid (support can get you a build it isn't released yet.) PPro's QuickTime I/O does seem to be 8-bit, yet AE is 16-bit and works fine.

This was my initial reaction. However as I mentioned before When I do the same conversion with any other clips I get 23.976 reported. With this particular clip I get 23.980 reported and also an error from After effects Adobe After Effects error: overflow converting ratio denominators ( 17 :: 19 ). Premiere pro also shows 23.980 for the clip in question.

Use AVIFrame.exe ( free tool) to check and or fix the frame rate of the source AVI. Yes it should be 24000/1001 but some app use other approximate ratios like 23976/1000 or crazier. One of these ratios is likely confusing QuickTime.