When running Movie Render Queue job for a sequence which uses FKControlRig and a sequencer window is opened, Track->ReplaceControlRig() is called every single frame, not only an initial frame. This sets CompliledDataManager->IsDirty and lets a sequencer reconstruct (every frame.) In a repro project scenario, custom track UMovieSceneTestInfoSection::ImportEntityImpl() is called every single frame. What issue happens is depending on scene setup and custom code, but this can cause that Movie Render Queque produces different results depending on whether a sequence window is opened or not. This behavior difference (due to a certain window is openning or not) should not exist.
Since it is not easy to prepare a scene for reproduce, please use the attached project for repro. This repro project does not include visual issue itself, but can prove different behavior in code level depending on a sequence window is opened or closed. It requires visual studio for building and confirming.
There's no existing public thread on this issue, so head over to Questions & Answers just mention UE-200776 in the post.