It's not a bug. That flag is maintained per session, by design. If during this session, if you say "don't notify me again", we don't bother you again for that specific Designer session.
The question was how long do we maintain that state. What if you create 100 new warnings? Don't bother letting you know in the middle of a runtime edit? Which warnings/messages from 5 months ago do you need to not care about and which new ones do you need to know? If we made that checkbox lifetime last a lifetime, there might be some critical warnings that you would miss in the middle of that 2AM runtime edit.
Hence, we decided that the lifetime of that checkbox was ONLY during that session. Not a global option. Not a part of the project.
BTW, we have implemented a much better mechanism for handling the root issue - that there are some messages (and even warnings) you KNOW that you do not need to care about. In the next release, you will be able to IGNORE any specific message or warning at one of 4 different scopes:
- Rung Level
- Code-Block Level
- Project Level
- Global Level (across all projects on that PC)
Once you can do THAT, you can intelligently ignore specific warnings/messages, and if the Program Check at Download dialog DOES come up, you may want to re-visit that code and/or tweak the "ignored" state of those specific rule "violations". (You can still "ignore" it during that session).