I'm on Chinook, and am still having this problem too (not being able to save configuration preferences). In fact, I thought that a work-around would be to create a "template" that contains all of my preferences (line weight, line color, etc). I saved the template, closed the program, then re-opened the template...it did not remember the config preferences.

This app has much promise if users can get past this problem.
Any guidance will be appreciated.