I'm working on animated text shown over a video. Textes are shown on three different moments, over a white background. To get my stuff organized, I created three scenes, and set my text on each one of them. First scene worked really nicely, I had no trouble at all, and could easily render the video with text on it. In second scene, Text was shown on screen as expected, until I animated it. After setting a simple 4 keyframes "get in screen - stand there a couple of seconds - get out of screen" animation, text just dissapeared fron render. When deleting the first keyframes (the ones that set text origin location), I got it to be shown on render, but it just kept on there and didn't get out of screen when it should. That's what you should see on the .blend file I upload, action keyframed on frames 1560 to 1581 is not rendered.
This is a screenshot where you can see the difference between what is shown on 3d editor and what is shown on VSE previsualization. Render acts as shown on VSE previsualization.
EDIT - My problem is not about having the scene overrid by a strip from VSE. The scenes are set on VSE over video strips, and can be seen correctly over video on render. My problem is about not knowing how to handle animation timing with various scenes on the project. I set markers on VSE and then used them as a guide to keyframe animations. This works well for my first scene, but my second scene seems not to match with timeline, I just don't know how to properly sync the scenes on the project.