Thanks for your bug report. The item 34 change is indeed the reason for this.
In previous versions, the decision of when to close a non-joined channel window was applied in contexts that had been added over many years. The item 34 change tried to limit and standardize this to the IRC options keep channels open settings.
These settings are actually applied in fifteen different numeric events relating to issues with trying to join channels.
I am going to change this in the next beta so that if you have either of the IRC Options keep channel opens settings enabled, non-joined channels will not be closed in these numeric events.
This should cover just about everyone who wants non-joined channel windows to stay open forever.
