I have the same problem as in post above.
A grey background of overlayed video covers another 2 videos in splitscreen.
I was trying to manipulate with blend properties, but no result.
I also use keyframes in this project.
It would help a lot if you shared a screen capture of your entire Shotcut window. Including the timeline and the Filters panel. Make sure the clip that overlays another 2 videos in splitscreen is selected.
I suggest putting your audio track on an audio track. Currently, your audio is on a video track, which you have hidden. Other than that, your screenshot is not revealing anything significant.
If that doesn’t solve your issue, you may want to upload your MLT project file here in the reply window. None of your media files are needed. Other people here can use their own media to help find a solution.