Try applying the letterbox aspect ratio effect to the 4:3 clips prior to export. If that fails...
THE best way to sort this out is to share your project, so others can analyze it. The process isn't difficult.
Here's how... http://nch.invisionzone.com/topic/23659-tips-for-getting-help-on-this-forum/
If it contains sensitive material you can link it in a personal message (PM) to me, via the envelope above. Be sure to FILE|SAVE PORTABLE PROJECT AS, not simply SAVE PROJECT, and don't forget to share it.
It's best if we can see the entire project, but if it's lengthy, save it and then split out and delete portions that look good upon export, leaving the 4:3 clips and a few 16:9 that do not. Export those.