Hey, sorry this post is a few months old but I wanted to post the solution for anyone else even if you found a workaround - There is a bug (at least as of 4.26) that seems to reset the show flag settings on instances of actors that contain a scene capture to the default settings that actor had when it was first placed, whenever the editor is reopened OR in packaged versions. As a result, scene capture instances that were placed before the parent was modified will have the settings they had when they were placed, regardless of the parent’s current flag settings.
The fix for me was to delete and replace all instances of the scene capture actor whenever I make changes to the flag settings. Slightly annoying, but does seem to fix the issue!