This is "normal" for 3.1 API based workbenches.
On later OS variants, like AmigaOS4 and probably MorphOS too, intuition message the apps to close (if they are based on window class and similar ) and so the problem only occurs for rarer programs that might have a stray lock on the Workbench screen.
Given time AmiBench will do the same, but just at the moment I haven't had tie to deal with this.
1280x1024 should work OK once saved though, it did on my test a while back.
