
The only main diffeence I can see between the two clips is the encoder profile, which is Main 10@L5.1@High on the source MOV and the Handbrake clip, but it's Main 10@L4@Main on the VD2 clip. I changed Handbrake's settings to use Main 10@L4 with the max bitrate, but it didn't help.
The other difference is that Handbrake is using the isom codec while VD2 uses mp42.
In the meantime, I've uploaded the MOV-to-MP4.vproject file to the OneDrive folder. Simply import it into VD2 (File | Load Project) and then use Save Video... (F7) and tell it where to send the converted clip.