Editing iPhone footage in final cut pro

So my sister got baptized and I'm trying to put together a hightlight of this awesome event. I did not have my video camera on me, but I did have my iPhone. I shot a 3 minute video and then brought it into FCP without any issues. It plays perfectly in the timeline, or so I thought. I'm letting the timeline adjust itself automatically to format to the iPhone video settings. 640x480, H.264 encoding. I have to render but that's only because the audio.
The issue I'm having is with the transitions from video to still pictures I imported from another camera. I'm adding a simple "fade in / fade out" and it's doing crazy things to my work flow. The video now jumps or lags and will not play smooth. Also when I transition into a picture from video it flickers real bad. I've tried everything and can't get it to work. Last night I started using iMovie and that was terrible. I need some help on workflow here. I should be able to go in and out of video and pictures without any problems. My exported video even jumps so I know there is something wrong. I tried just putting two iphone video clips back to back and there was lag there as well. I edit HD footage all the time and have a loaded system. So I know it's not hard ware...
PLEASE HELP!
MacBook Pro 2.4 15" 4 gig RAM Mac OS X (10.5.7)

Convert the video in Compressor or the QT Pro player to motionjpeg or some other editing format.
Use that instead.
Remember that the original footage is heavily compressed and using a transcode won't improve the footage, just the edit.

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Editing iPhone footage in final cut pro

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