Missing Audio with Merged Clips

I'm experienced a very confusion and frustating kink in clip merging process. I suspect other people have encountered it before, but I can't find where. I'll post tech details at the end.
I merged clips by marking an in point on the audio and an in point on the video. I placed both clips in to my timeline. I deleted the stereo track that came with the video. I linked the 4 mono channels to the video, and dragged them over to a bin, where it asked me to name the merged clip, and I named it according to the scene.
I had no problems working with them
Upon returning to my work, however, some of the audio seems to be missing. That is, the top of the four mono tracks is there, but the other three, while there in the timeline, play no sound - they don't have any waveforms anymore (it is not any kind of mute track issue, the waveforms themselves are gone).
I have since tried merging clips directly in the media browser, using in points, and this seems to resolve the problem. While I am happy to see a solution for the future, I am on a very tight deadline and don't have the time to re-merge all of my hundreds of clips.
This is an awful bug that Adobe has got to fix.
Thanks!
Shot on canon 5D
From Properties:
"Type: MPEG Movie
File Size: 1.3 GB
Image Size: 1920 x 1080
Frame Rate: 23.976
Source Audio Format: 48000 Hz - compressed - Stereo
Project Audio Format: 48000 Hz - 32 bit floating point - Stereo"
Audio on dual system (unsure of which model):
From Properties:
"Type: Windows WAVE audio file
Source Audio Format: 48000 Hz - 24 bit - Mono
Project Audio Format: 48000 Hz - 32 bit floating point - Mono"
Premiere Pro 5.5, most recent update.
Windows 7 Home Premium 64 bit, most recent update.
ASUS G53JW
Intel Core i7  Q740 @ 1.73Ghz
8Gb Ram
NVIDIA GeForce GTX 460M

I created a new user account and trashed my preferences and I have the same problems. I created a new project, and new sequences. Same problems.
It only happens with 23.98 (batch reverse telecined using Cinema Tools) NTSC DV clips that have been merged with separate 24-bit 48 khz Quicktime audio clips (converted from BWF using BWF2XML). Clips that were captured from the tape with audio and video simultaneously don't have this problem. The discrepancies between the actual amounts trimmed and the white numbers in the trim windows are consistent. If it's off by 6:10 on a clip, every time I try to trim that clip it will be off by the same amount. But the number varies from clip to clip. It's generally 5-8 seconds.
If I try to trim only the audio, I don't have any trouble. If I trim the audio and video at the same time I don't have any trouble. It's only when I trim the video on its own. If I use the original video clip before it's merged with an audio track then it trims fine. If I cut the merged clip into a sequence then delete the audio track from the sequence the problem remains.

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