This sounds like your timeline/sequence has been set up incorrectly. An early problem i encountered was understanding the difference between setting up a Sequence at the right scale for the footage im using
setting up your export settings to co-respond with my desired output ( i.e. output to dvd or youtube or etc...).
In short; This could be a problem with the way you have set your original sequence/timeline.
I posted a quick rundown on how to get this right in this post:
Have a look i see what you think.