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double click the sequence in the timeline to open it in the viewer window (left). Click the Effects Tab. Make sure that the sequence actually has the video effect on it. you may have applied the fx in the viewer in a way that it didn't actually get put in the sequence.
Make sure that when you're exporting that you have the sequence you want to export highlighted with proper in and out points and that all relevant tracks are also lit and unlocked.
Try exporting a small bit my making an in and out point and exporting outside of compressor (say to Quicktime) to see if you get the same results.
Leaving anything out? Weird plugins?
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