One suggestion to help isolate certain DT/DN problems (e.g. Disappearing Sorter) that may be side effects of interactions with other apps:
• Temporarily disable Login Items by holding down the Shift key during login until Finder launches
Then launch the Login Items individually and check if they’re interfering with DN/DT.
Another trouble isolation method I use on Leopard is to temporarily run apps under the generic Guest account. That often helps determine is it’s a general problem or something specific to my account.
This applies to any app, not just DT/DN.