Rendering rearranges my timeline!

Hi
I have an annoying problem when it comes to rendering my film (shot and transferred from a Nokia N95 to FCE).
Initially i used simply 'fade in fade out' transitions between each shot, but found that when it came to rendering the video in preparation for writing it, the rendered film was different. FCE seems to start each clip about two seconds before it should start, and end it two seconds before it should end. So if i shot someone saying the alphabet and chose the sequence from c - g in the timeline, once rendered the film would show the sequence from a - d.
I've taken out the transitions and done them manually by dropping keyframes, but the same thing still happens. It is very frustrating!!
Can anyone help?

i'm gonna update this again as I've played around with everything for the last few hours and got nowhere. I'm worried there's an issue with the file itself, although I really don't know. I'll detail everything i do/know below, and any help would, as ever, be greatly appreciated.
this is what i do...
I'm working from an N95, which transfers to my mac in mp4. I convert the file using MPEG streamclip, using the Apple DV-PAL codec, leaving the frame unscaled at 640x480.
My FCE easy setup is DV-PAL. I import the clip and drop it into the timeline. A warning sign comes up that says 'Attention this clip does not match this sequence's settings or any of your sequence presets. Change sequence settings to match the clip's settings?'. I click Yes.
When it comes to writing the video at the end, i've tried using 'none', 'DV-PAL' and 'apple intermediate codecs'. each one corrupts the transitions, even when i'm lowering keyframes instead of using an fce transition.
here's what i know...
i've tried doing things without any graphics and the same thing happens (so my above post can be ignored!!).
every single transition gets corrupted.
if i don't change anything, as in simply leave the clips with abrupt edit between, then writing to video works and nothing gets distorted.
as soon as i do try and impose a transition edit, the transition gets corrupted. it moves the start line back a bit (even after using the ripple tool and adding 15 frames) and often jumps between its own frames, creating a strange double-take effect. using alphabet analogy, it often goes a-b-c-b-c instead of a-b-c!!!
any ideas??? sorry for the essay, just need an answer and quick as working to a deadline and thought it best to put everything down. hopefully i'm doing something stupid and this can be sorted easy and quick!
thanks

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    I understand that, being an "Unkown Errror" Adobe does not have a iniversal fix, but please don't ask me why I want to output my timeline.
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