Publisher version 1.8.2.0
Steps to reproduce:
Right-click any Vendor in the tree and "Exclude from being enabled during SCCM inventory scans"
Apply settings
Close Publisher
Re-Open Publisher
Select App underneath the above-disabled Vendor tree
Right-click App, uncheck "Exclude from being enabled during SCCM inventory scans"
Apply
Check box next to App to enable
Apply
OK to close Publisher
Re-open Publisher
Find App
App is not enabled and the "Exclude from being enabled during SCCM inventory scans" box is still checked.
Please see this GIF of steps captured
https://gfycat.com/untimelysprycaudata