I presume that you only experience the problem when switching directly from System 6.x into Mac OS 8.1? Desktop Manager fixes the ability to switch between System 6 and 7.x in either direction. And problems should be rare when switching in either direction between System 7.x and Mac OS 8.1. What is the experience when switching from Mac OS 8.1 into 6.x?
If my summary accurately describes your experience, the obvious thing to do is to avoid switching directly from System 6 into Mac OS 8.1, using System 7 as an intermediary boot stage. Unfortunately, you'll just have to remember not to do the things that cause problems.
Programatically, a partial fix is possible. You'd need to write an INIT (or three) that checked for a flag indicating which OS version was last used to boot the Mac. If the current OS was 8.1, the INIT would halt the boot process before the Finder launched (the Finder and an associated service manage the desktop files which cause the problems you see), display the Startup control panel dialog and force a reboot before problems are created.
Hacking the Desktop Manager to recognise Mac OS 8.1 is also a possibility, but it may not be trivial.
If my summary accurately describes your experience, the obvious thing to do is to avoid switching directly from System 6 into Mac OS 8.1, using System 7 as an intermediary boot stage. Unfortunately, you'll just have to remember not to do the things that cause problems.
Programatically, a partial fix is possible. You'd need to write an INIT (or three) that checked for a flag indicating which OS version was last used to boot the Mac. If the current OS was 8.1, the INIT would halt the boot process before the Finder launched (the Finder and an associated service manage the desktop files which cause the problems you see), display the Startup control panel dialog and force a reboot before problems are created.
Hacking the Desktop Manager to recognise Mac OS 8.1 is also a possibility, but it may not be trivial.