Glitches exporting in FCP 7

Hi Everyone,
As an experiment, I recently shot a very short film on the iphone 4S. Before importing to FCP, I converted the footage to ProRes 422. I also used a shotgun mic(non phantom powered) plugged into the audio jack for sound. The footage looks fine, but the audio is out of sync. Not a problem I resynced it.
I cut the film(a minute long) and put some music to it. In the timeline it looked fine until I exported. This happened: (it's a 6 second clip)
http://www.youtube.com/watch?v=xCHwEnBKM9I ***Note - inappropriate language***
As you can see, there is some sort of ripple at .02. This happens when you focus with the iphone. In the timeline, I edited that clip to exclude that focus zoom in/out. It's not in my timeline. Also, you can hear the audio is out of sync. What's more is the actress stands up before answering the door which is obviously cut in this export.
I have exported this in compressor several times to no avail. I have recut the clip in the viewer and brought that into the timline to no avail. I have tried to export with the original unsynced audio to no avail. I shut my computer down, restarted, exported again to no avail.
Sometimes when I play back the video in the timeline other clips get glitchy. For instance, in the middle of one clip there seems to be a jump in the cut as if I took out 3 frames( I didn't.) I can fix that by recutting in the viewer and bringing it back down into the timeline. So that cut might be fine, but the same thing sometimes happens to another cut.
sequence preset: prores 422 HQ 1920X1080 24P 48 kHz
frame size: 1920x1080
aspect ratio: hdtv 1080i (16:9)
Pixel: square
timebase: 23.98
I don't know if it's my computer(5 yrs. old), FCP 7, which has been fine up to this point, or I messed up my settings somewhere. Not sure what else to try.
Thanks for taking a look.

Mpeg streamclip isn't allowing me to convert the audio to the specs you mentioned WHILE converting the video to Prores. Is there a way to do both at the same time or do you have to do both separately?
When I originally converted the video, the audio was converted to a 44.1k 16bit. I went ahead and converted it into 48k 16bit aiff as you had mentioned. I synched it back with the original clip and the problem still exists.

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Message was edited by: Eric Pautsch1

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Glitches exporting in FCP 7

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