Trouble Shooting:
Control Commander not showing up in the Control Panels folder:
Control Commander is an Application, not a Control Panel, if you just drag it onto the System Folder it will not "autoroute" to the "Control Panels" folder.  To get it in there, you need to open the System Folder and drag it into the "Control Panels" folder by hand.  Given what the application does, consider putting it into the "Apple Menu Items" folder instead.  If you would like to know how to do this, read the tip on "Putting Control Commander into the Apple Menu".

Control Panels not showing up right in the list:
Control Panels whose names contain multiple leading Tab or a Return characters, or multiple adjacent space characters, will show up as "unavailable" in Control Commander windows.  To access them from Control Commander, you must change their name.  An exclamation point (!) makes a pretty good replacement for these characters, but look at the documentation that came with the particular control panel to see whether there are any restrictions on changing its name.  The order in which Control Panels load into memory is determined by their names, and some Control Panels need to start up before others.

Descriptions not showing up right in the list:
If the name of a Control Panel isn't the same as the name that appears in the Control Commander Commands file, the lines describing what the control panel can do will not be attached to the Control Panel. They'll either not be there at all, or they’ll all seem to be “unavailable".  Control Commander actually allows for a bit of slop in the names of Control Panels to account for special characters at the start of a name, but too many changes can confuse it.

If the lines describing what the Control Panel can do are there:
The name of the Control Panel causing the problems will show up twice in the text. Once with the correct spelling, but with no description lines, and once with the incorrect spelling and a description of the Control panel. Cut the line with the correct spelling, and paste it over the incorrectly spelled line. Then choose "Save Text as Commands File" from the File Menu. This should fix the problem.

If the lines describing what the Control Panel can don't show up even as "Unavailable" choices:
The Smart Merge option will not allow the description for a Control Panel to be added to the Commands List unless there is a Control Panel with the same name installed on the computer.
Open Control Commander and choose "Get Control Panel Names" from the Edit Menu.
Find the name of the Control Panel in question and Copy it.
Open the file that contains the description of the problem Control Panel. [It's usually "Descriptions 8.1" or "More Descriptions" in the "Control Commander Files" folder].
Find the name of the Control Panel in question, and paste the correct name over it.
Save the File, and close the "Control Panels On ....." document.
Display the Main window by choosing "Show Command Window" from the File Menu.
Choose "Add Descriptions...", and add the file you just corrected.   This should fix the problem.

Cleaning up a messy Commands List:
If the list in the main Control Commander window is starting to look ratty, you can clean it up without having to start all over.  Here's how it's done:
Choose "Get Copy of Commands File" from the Edit Menu.
Hold down the option key and click on the "Tools" button.
This will remove any unavailable Control Panels from your document.
Click on the "Tools" button and check All the boxes.
Click "OK"
If you've still got junk in the document, delete the offending lines as you would with any text editor.
Click on the "Check Syntax" Button in the top left of the editing window.
Fix any lines that contain errors.
Check the Syntax again.
Choose "Save Text As Commands File" from the File Menu, and the garbage disappears.
-Editing Must be enabled in order to do this.
If this happens often, you can prevent anyone from messing with your Commands List by setting some of the security options in the Preferences Dialog or elsewhere.