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Luke,
It sounds like your sequence settings don't match your clip settings. When you place a clip in the timeline does a green bar appear over the clip? If so your sequence and clip settings don't match. You have two choices, force it to render or use Auto Conform Sequence. I suggest the latter.
You can enable Auto Conform by going to your User Preferences Auto Conform is in the Editing Tab, bottom right. Set it to Ask. That way when you add a clip to a new sequence that doesn't match you'll get this message:
For best performance your sequence and External Video should be set to the format of the clips your are editing. Change sequence settings to match clip settings? Yes or No. Select Yes and your clip should match the Sequence Settings. Keep in mind that this only works with a new sequence that doesn't have clips already added. If the sequence matches your clips then you won't be asked to conform.
Possibly the reason your export looked good is that it was rendered in the export process.
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