Are you in the MATCH MONITOR mode? Click the chevron to the right of the View button. This may give a better representation of what the export will look like.
Try using the LETTERBOX or CROP TO ASPECT RATIO in the effects window for the clips that aren't correct. On export do the same.
If you upload the project, share it (make it public) and post the link here someone will analyse the issue. It's easy, and can be private...
Here's how... http://nch.invisionzone.com/topic/23659-tips-for-getting-help-on-this-forum/
If it contains sensitive material link it in a personal message (PM). Click the envelope above. It won't be passed on or retained.
Use FILE|SAVE PORTABLE PROJECT AS, not simply SAVE PROJECT, and don't forget to share it.