Its not the amiga screenmode that gets changed. Its the output driver of the Mk2. That damn config tool is a real pain in the ass to work with I tell you.
If you delete the monitor driver in Devs:monitors you wont have the screenmode available to you.
You are confusing the native amiga display modes with the indy mk2 modes (since you are outputing from the dvi output not the Amiga RGB out)
You are going to have to configure the correct mode in the indy prefs
