Hi JFlatz, sorry, I never received a notification for your report, I just happened to update the plugin yesterday and was checking the page today and saw this report.
I’m not sure I understand what is happening for your install. are you saying that after installing it, you did not change the menu for any individual pages yourself but that they are being changed anyway? That should not happen if so.
My update yesterday added support for multiple menu locations on a given page, so you can target which location you want overridden. Can you update the plugin and check it again to see if you still have the problem.
Again, sorry I did not get a notification about this report.