I have 9.10 Karmic and 10.10 Maverick systems at hand and if I start onboard from the terminal I got the same warning on both of them as well: "WARNING:Config:Can't load Default loading default layout instead" on both systems. Here is the screenshot from the Maverick fresh installation:
What does that warning mean? I'm not sure but I feel that its something related with the keyboard layout. I use "Turkish Q" layout. That warning might try to say that "there's a Default layout for onboard but, for now, not that Default but your default layout will be started". If this is the case, obviously, it makes sense. However, I have no clue what the "main Default" is or what to do in order not to get that warning, but -at least for me- that warning has no ill effect and I didn't even know about such a warning before I read your question. (I don't start onboard from terminal so I haven't seen it.) In my opinion that is not the important part of your problem or maybe its not an issue at all.
Your second and main problem: You say that onboard crashes when you minimize it. On my Maverick system, when I minimize onboard (version 0.94.0), its icon still lies on the bottom panel as usual for most of the programs. Like this (circled in red):
But on my Karmic system (onboard version 0.92.0) it behaves in a different way: When I minimize onboard , its icon sits the top panel, right side. Like this (circled in red):
On Karmic, with onboard version 0.92.0, if this is not set to be on top panel, it crashes when onboard is minimized. Most probably, this is a bug. So, on Karmic, I set it to be on top panel. On Maverick, with onboard version 0.94.0, both ways work, as it should be, so its up to taste to choose one or the other behaviour, i.e. minimizing to top or bottom. It may be possible to uninstall 0.92.0 and install 0.94.0 on Karmic but I didn't try it and I don't know if there are dependency problems or not.
So, from where can we set this behaviour? Let's go to the Settings section of onboard. How? Start onboard (version 0.92.0 in this example) and click on the area circled in red:
Now click on the Settings :
Tick the option "Show icon in system tray to hide/show onboard":
Settings interface for onboard 0.94.0 is a little bit different, but the same choise exists as shown belown (remember that on Maverick with v. 0.92.0 that choice was a must as a workaround to prevent crash; here it is optional as an option should be):
In short, in your situation (Karmic + most probably onboard v. 0.92.0) I advice to tick that box. Then, you don't have to start it from the terminal; you may start it via Alt+F2 or via Applications menu (if you have added onboard to the menu.)