The Mp4 video was created from the project files that you uploaded: two clips and the.VPJ data file. Starting with a clean slate, try this approach...
Apply effects to the master clip until it is scaled, rotated, cropped, etc. just as you want it. Crop out any random pulses at the top of the raster. This is sequence #1. Then click the + sign on the tab above the timeline to create a new sequence. The timeline will be cleared.
Up in the media area click the SEQUENCE tab and load sequence #1 onto the timeline. Now make your cut/s, and then export this completed sequence #2.