Would this actually be version 8.45?
Export will output all tracks in the sequence. Did you scale down the size of the overlay videos so lower tracks would be seen in the background (picture-in-picture) ?
The best way to resolve this is to share. It's easy, takes little time and can be private. Just follow the PORTABLE project instructions here, so we can see what you see. Don't upload the export.
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 get a shareable link to post.