Back to basic set up.
Set up the dialogs you want to see on start up. Size them to suit. Select the dialog (layers) you want to start with.
Select the tool you want to start on (brush tool). Select the brush (round), pattern... you want to start with. Set the size you want to start with..etc
optional - the little arrow in each dock and 'lock tab to dock'
Then Edit - > Preferences ->
1. Tool Options, untick save on exit (if ticked) and save tooloptions now
2. Window Management untick save window postions on exit, click on save window positions now.
Ok everything to back out.
edit: This for windows but equally valid for linux
https://www.youtube.com/watch?v=ZQz0zCyVFJU 4 min