I've noticed the following behaviour of DOpus under Vista. I don't have DOpus automatically starting when Windows starts.
When I click the DOpus icon either on the Start Menu or on the Quick Launch toolbar, there is drive activity, but DOpus doesn't appear to open. However, dopus.exe and dopusrt.exe are running in Task Manager.
If I then "start" DOpus a second time, it appears on the screen immediately.
This problem only happens the first time DOpus is opened after the OS is booted. If I close it during a session and then reopen it, it works fine.
Do you understand that closing a DOpus window is not the same as "closing" the whole program? When you close a lister window, the DOpus process and DOpusurt.exe are still running in memory (and if you have the system tray icon turned on, it will still be there). Because you are not running it at startup, the first time you run DOpus it has to start those two processes before any lister windows can be opened.
Now, you said you have it set to open listers that were open the last time DOpus was shut down. I'm not sure, because that's not how I have my DOpus set up, but I believe that means listers that were open when the program was completely quit (IE, quit from the system tray or listers that were open when windows was shut down). Try leaving a DOpus window open, shut down Opus from the system tray icon, then start it again and see if you get your lister back.