I have exactly the same audio issue, that has started only recently. I have successfully imported 1080/50p video from my Panasonic HDC-SD90 camera in iMovie11 after rewrapping with Alan's script on April 26. All with no audio issue what so ever. (and using an old Perian 0.5 version). I did have issues with the time code; all my clips where out of chronological sequence after shutting down and restarting iMovie. They now seem to be in order of clip lenght, although not fully consistent. But that's another story.....
I first experienced the audio issue on May 8, when trying to import new footage I shot the day before. I then reinstalled Rewrap2M4V and the latest version of ClipGrab and installed the latest Perian version. Still to no avail. When browsing the system profile -> Software -> Frameworks, I did notice that the AVFoundationCF was updated on March 31 2011. I'm not a developer, but this seems to be the framework used for audio / video playback for (most) Mac OS X applications such as QuickTime, Quick Preview and iMovie11. ('he AV Foundation framework provides an Objective-C interface for managing and playing audio-visual media in your Mac OS X application.') I do suspect a version conflict between some components, but it seems the latest system file updates date from April 17 and they seem unrelated to my layman's eye. Also these dates do not match the time the audio issue has started. Maybe Alan Somers can shed some light on this subject?
I really hope for a quick solution, because converting to H.264 25fps is no option for me. I really mis the smooth playback when doing this, especially when using slow motion.