There are a few annoying settings that do not stick. I am using the Git build now so this is up to date

1: Hide Statusbar (Statusbar will be shown again upon the next time the program starts)
2: Hide File Toolbar (It can crop up again when workspace layout is switched or when program is restarted, I would like to suggest the removal of this feature, it's an outdated UI element that no program except for office programs use these days, it certainly has no place taking up precious UI space in a painting application)
3: Lock Docker (On my tools docker I get a blank space between the tool icons and the edge of my screen that I do not like. If I lock the docker I can downsize it horizontally the way I want it to, but the next time I restart the program this docker (and only this docker) will be unlocked again creating this blank space again)

It's also worth mentioning that lock docker should prevent resizing of dockers which it currently does not. However granted bug #3 i mentioned here, I'm kind of relieved that it doesn't prevent horizontal rezising right about now

Found some more info on this.

I noticed when I enabled hide docker, that the statusbar re-appeared as I closed the program (so I think that the problem is with some action the program executes when it closes, rather than when it starts up) it wouldn't be surprising if it's the same for the other 3 although I didn't have a chance to check that.