Pro Tools files imported to FCP X causing QuickTime movie problem

Well 2 days later and hours on the phone with Apple tech support Senior Advisors, and problem still not solved. HELP.
Everything works fine in FCP X, but when I create the QuickTime movie, it is way out of sync (by many seconds).
We have isolated the problem to audio files that I am exporting to Pro Tools, processing, and then importing back into FCP X. I can create a QuickTime movie with the original video/audio and it is fine.
Information
The original video came from Canon HF M40 camcorder: AVCHD (using MPEG4-AVC / H.264 compression codec), MTS format. Audio is 48kHz, 24 bits.
I used ClipWrap to rewrap the video into ProRes 422 and decompress the audio and save as LPCM.
I simply provide this FYI. As I said earlier, the original video works fine and the resulting QuickTime movie works fine. So the original files imported into the FCP project are not the problem.
The creation of the problem audio occurs as follows:
- Detach the original audio from the original video, and export
- Import this audio into a 48.0 kHz/16-bit Pro Tools HD session and EQ/limit the audio
- Import the resulting audio into FCP X (exact same length file, audio waveforms aligned with the original audio).
This audio works fine in FCP. It is in sync with the video, everything looks great.
I ran Pro Tools at 16-bits because a senior advisor told me FCP runs at 16-bits but does not convert imported stand-alone audio (as opposed to combined video/audio) to 16-bits; thus the Pro Tools session had to be at 16-bits. I changed from 24-bits to 16-bits, and this didn't solve the problem. (FYI, when Pro Tools imports the original audio exported from FCP, it says the audio is 24-bits, not 16-bits).
What is the problem?
The basic question is why does this audio cause QuickTime a problem?
Something is going on in the conversion to the QT movie. In FCP X, I don't have a way to play with the conversion variables except to set "Video and Audio" and "Use current settings" (which is ProRes 422).
The only difference I see between the original audio and the Pro Tools audio is that the original audio is stereo and Pro Tools works with dual mono files (L & R). The mono files work fine in FCP and I can't imagine why QT would have a problem with these, but I haven't tried converting the files to stereo before importing into FCP.
I should also mention that I selected the stabilization and roll correction algorithms in FCP. I assume these don't create problems in QT. I mention this because I didn't use them when I tested making a QT movie with the original video/audio files.
FCP and Pro Tools are used together all the time to do exactly what I am doing......improve the sound of the original audio. They are the premier video and audio professional programs. Of course, the final product is often not a QuickTime movie, but many times it is a QT movie.
What the heck is going on???
HELP.

(1) It is immediately out of sync. It even appears to be speeded up to me initially, but this is subjective. But it is clearly out of sync throughout, not a gradual drift.
(2) When I create the audio files in the Pro Tools session, the files are automatically stored in the audio folder of the Pro Tools session. So I don't actually have to go through an export process. I just close the Pro Tools session, then open FCP X and import the audio from the Pro Tools folder.
I'm not sure what additional specifications you seek, other than:
- wav files
- sample rate = 48 kHz
- Bit rate = 16-bits (and earlier I used 24-bits)
- Files are dual mono, rather than stereo (name_01.L.wav, name_01.R.wav). As I mentioned above, I have not yet tried converting these to stereo before importing into FCP, to see if dual mono causes an issue with QT. It does not cause a problem in FCP. I will try this today if we don't solve the problem.
(3) I can upload a portion of the audio to a server and send you a link to the file so you can download it. Is there a way to private message on the forum so I can get an email address to send you the link?
(4) The original video came from Canon HF M40 camcorder: AVCHD (using MPEG4-AVC / H.264 compression codec), MTS format. Audio is 48 kHz, 24 bits.
I used ClipWrap to rewrap the video into ProRes 422 and decompress the audio and save as LPCM.
The FCP Project was set up at:
- Starting time code - 01.00.00.00
- Format - 1080p
- Resolution - 1920 x 1080
- Frame rate - 29.97p
- Audio channels - stereo
- Sample rate - 48 kHz
- Rendering format - Apple ProRes 422

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