Thanks for the bug report, and apologies for the slow response. This thread has only just come to my attention (for future reference, bug reports sent using the email link on the Settings > Page Lists Plus page in the dashboard will reach me more reliably).
The issue that you're seeing is to do with the "Exclude children of excluded pages" option, which is a fairly recent addition in response to a user’s request. I realised that this feature was working in a way that most users would find irritating, and so a couple of days ago I released an update. In the latest release, the "Exclude children..." feature is still there for users who want to exclude a whole section of their site (temporarily enable this, exclude the section, and then disable it), but now when PLP is installed the feature is disabled by default. That should work best for most users.
Users experiencing problems like that described above should disable the "Exclude children..." option. New users shouldn't experience this problem at all.
I hope that helps to clear up what's going on, and apologise for any inconvenience caused.