I've been pulling my hair out all afternoon looking for a cause and a good solution for this problem. I have video shot with a Canon 5D Mark III, and audio recorded to a seperate Zoom audio recorder at 24bit/48kHz WAV files. I've got them all edited together in Premiere (with seperate tracks for each channel) and the source audio track turned off. I placed short crossfades at many of the cuts in order to smooth out any difference in background noise levels and playback on the timeline sounds great. When the timeline is exported however, it seems to ignore some of the fades. I get pops that weren't there and there are a couple of spots where I cut from one shot to the other right before a person started talking, and I get a repeated audio hit, like it simply took both parts of the audio where the fade was and played them.
This is driving me crazy. I've exported to AIFF, h264, and Quicktime ProRes. I've tried importing the project into CC on the Mac, CS6 on the PC, Exporting to an XML file with only the audio and bringing that into Final Cut Pro 7... that relinks things very oddly, including one or two clips timing being totally out of sync and throws errors relating to the sample rate not matching (when it does).
The only thing I was able to do for now was to pull the clips into seperate tracks so they weren't touching and add in fades there, which seemed to help, but that isn't a good solution.
Does anyone have any ideas as to what might be causing this and how to fix it? Thank you for any help you may have.
MacPro 2,1 with 16 GB RAM, running 10.7, Adobe Premiere Pro CS6. Project resides on a RAID drive connected via fibre.