Hi TJ,
It's hard to diagnose your specific problems without more details. For the moment, let me give a few fundamentals and see if this helps. (We can go into the specifics better via Personal Message if necessary.) If nothing else, this roadmap might help someone else.
1. Download and install the Duenna. Start with the Full Installation (Rev.44/13, Feb 2004). You also need FSUIPC (either registered or unregistered).
http://johannesmueller.com/fs/web/duenna/
--Then add the latest Update (Rev. 131/30, Jan 2010) to update the already installed full version.
--That is, you want the original full version and then the latest update. (The update is cumulative. No need for the intermediate versions).
2. Click the Settings button and another panel will open. Pick a user name and an event. (Here it is "2013 western roundup") For the moment when you are testing, you need not have your flight tracked, but when you start flying officially, you want the Duenna to send data to the Duenna server to keep a record of you flights.
It sounds as though you have already done this. Now proceed to get the realism settings in good order.
3. Make all the correct settings adjustments to FSX (or FS9). For the sliders, be sure that they are at the end of the continuum. Then set up and use MSFS real weather with 15 minute updates. (For the moment, don' t use Opus.) Save your current flight as the Default Flight, now with the correct settings. Close out the simulator.
Then restart with your newly saved flight. Check the setting to be sure that they are correct. Once you are confident that everything is right, start up the Duenna. Things should be ok. (The Duenna reads some of the settings from a stored record of your previous flight.) If errors persist, check the Duenna log file (the textfile) to look for hints about what is wrong -- often the Duenna will complain explicitly about specific settings. If problems continue, then we'll get someone on this as soon as possible. Let's get the basics right before we start to use another weather engine.
4. If you want to use another weather engine (such as OpusFSX), then you may discover that the Duenna registers yellow (not green) on the takeoff...while complaining about the weather. Go ahead and fly. The Duenna will give you a green clearance when you complete the flight. Again, if this does not work for you, we'll get some help to you.
Once we get this sorted out, you might find this little program to be a gem. We owe a debt of thanks to Johannes Mueller for his splendid work.
Best,
Mike