Is there a menu selection that saves the pane layout between program starts so I do not have to manually re-arrange after every re-start?
What exactly isn't being restored properly? Most, if not all of the UI should be restored properly unless a Force Quit is performed.
You could also use File > Save Workspace but that's not restored automatically at start up...yet:
File > Save Workspace
Ok - thanks Carey. I just ran a test and all the settings were retained. It must have closed via a forced quit which then caused it to loose some settings as you pointed out.
Just an FYI, we are working towards having a force quit recover be a little smarter so hopefully this experience will improve for you in Komodo 11. I'm glad it's working in a normal situation though.