Never experienced this with OBS(1) since you can just capture each Window and position them in OBS then have different scenes bound on hotkeys.
That's how I ended up recording my entire screen in the explanation video.
My main problem is I really don't like using OBS for pre-recorded content since the work flow to record a video is much less efficient than with Camtasia. Also when editing the video, Camtasia really chokes compared to using its format as a source file and you lose out on being able to highlight your cursor.