No you are not the only one with this problem! I was hoping that the last update would solve what appeared to be a random glitch with XDCAM HD & IMX Pal audio. Unfortunately Im experiencing all the same issues you report: audio drops out on playback or vanishes on export. The annoying part is that it appears completely arbitrary; some files play fine, others do not. My work around so far: export the finished audio edit to 5.5 using FCP XML, mix down and reimport. Hardly elegant or efficient, but at least a way to stop me banging my head against the wall.
Another alternative I’ve tried is to use 5.5 to rip the audio from the MXF files. Again, not ideal!
This appears to be a genuine bug, comparable with the famous ballooning .pr files in the first release of v5. That one cost me 2 days and a serious case of high blood pressure. Adobe are you listening…?
Andrew Crawford | 3rd Eye Productions Amsterdam
https://www.3rd-eye.nl