Media Encoder changes the timecode when converting to Quicktime ProRes 422 (LT)

After spending the majority of my day searching for a solution to this problem, I am hoping someone here will know how to resolve this issue.
After encoding several hundred clips of various file types to ProRes 422 LT at 23.976fps in Media Encoder, we discovered that the timecode of the source clips and the LT clips varies significantly when we bring the quicktime clips into FCP 7 or Quicktime 7. This is also creating issues for the EDL.
The source clips are XDCamHD, H.264, and .R3D files. We set up a batch in AME with a preset for ProRes (LT) at 23.976. After the batch processes, we import the clips into FCP 7 then export an EDL from the sequence. The EDL shows timecodes that do not match the source clips.
The timecode is off by several hours, not just a few frames. If we look at the LT clips in Premiere, the timecode seems to match the source clip. In Final Cut, not even close.
Any ideas on where to start on this one?
If we use RedCineX to convert the R3D files, things seem to work. Also, compressor seems to have correct results. We were hoping that media encoder would be the solution as it processes these clips much faster.
We are looking for a solution that doesn't involve re-transcoding all of the footage.

Two.
First, this.
http://help.adobe.com/en_US/premierepro/cs/using/WSd9957a95a81082eb28f05af5126718c47be-800 0.html
Second, this.
Customize or load keyboard shortcuts
From the Set menu in the Keyboard Customization dialog box, choose the set of keyboard shortcuts you want to use in Premiere Pro:
Adobe Premiere Pro Factory Defaults (Adobe Premiere Pro CS5)
Adobe Premiere Pro CS5.5 (Adobe Premiere Pro CS5.5)
Shortcuts For Avid Xpress DV 3.5 (Adobe Premiere Pro CS5)
Shortcuts For Avid Media Composer 5 (Adobe Premiere Pro CS5.5)
Shortcuts For Final Cut Pro 7.0

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