What is your operating system? Windows 10 Home
What is your Shotcut version? 26.8.1
Track V1: Any clip.
Track V2: A clip with transparency. I the case below, just a Text clip with a transparent background. But a .mov clip with transparencies will have the same effect.
Exported project when Processing Mode is set to Native 8-bit CPU (check the background when the playhead reaches and leaves the text clip).
No problem when Processing Mode is set to Native 10-bit CPU
This is similar to the bug reported here (which was fixed) but in that case the brightness filter was involved: