reproduced on Windows and Mac

To replicate with this project,
- open the Playmaker editor window, and dock it into your editor panels. (Playmaker menu)
this is a critical step which seems to cascade into problems at next launch
- create custom window layout in the editor and save it by name.
(I don't know if the order of the first 2 steps matter- maybe try reversing them if you don't see the problem below)
- comment out line 9 of the .cs file and save it. this intentionally introduces a scripting error, another required step to replicate the bug.
- save & quit the project.
- re-launch Unity on this project
you should see 2 things - an exception similar to what I pasted below, and the window layout is reverted to default, and picking your custom layout from the popup menu has no effect.