First, I apologize because i’m not familiar with technical terms. I’ll try to describe the issue as accurately as possible, but please feel free to ask for more details if necessary.
I cut an edit with 2 source clips. One was 542x432 H264 with 785x432 aspect ratio.
The second clip is 1280x720 H264 with 16:9 aspect ratio. There are narrow vertical black lines on both side of this clip, so I zoomed it in with Size and Ratio filter to hide those lines.
No matter which one I add to timeline first, the HD clip turns into pillar box (much thicker black pillars on both sides) with wrong aspect ratio in the final export.
I did the same edit in KDEnlive and the result was good.