Strange! You can delete PlayMakerWelcomeWindow.cs.
However I'd be worried that editor prefs aren't saving properly for you, for some reason, and you'd run into other problems later...
As an experiment try changing a Playmaker Preference (lower right corner of FSM editor) and check that it sticks.
I'll also double check that there isn't a bug in the Welcome Window script...
Also make sure you've updated to the most recent version of the beta (1.8.0f37)
EDIT: Nevermind, I found the problem. Will be fixed in the next update... thanks for reporting it!