It shouldn't happen, but I'm afraid the only thing I can think of is to add those black mattes.
I agree with Jim. Do not leave gaps in your Video. Instead, go to the New Icon at the bottom of the Project Panel, choose Black Video, and Trim that, to fill all gaps.
Good luck, and hope that helps.
I dont know if the gaps are the issue in your case... but to fill them easily and quickly.
Make one long Black Matte or Black Video and place it on Video Layer 1. (ie contiguous under all other video tracks)
Means shifting all others up or inserting a new layer as Video 1.
FWIW. I have never had issue with black gaps. ( Its only alpha)
One of our customers had this exact issue and it was defnitely the gaps in the timeline - H.264 exports would freeze frame on last frame before gap when played back in a media player. Editor had laid down VO and music tracks first and was then piecing together video to match and had some empty spots in video track and was just exporting "proofs" and did not think he needed the gaps filled in.