I managed to correct this problem on my machine. It might not be an elegant solutions for everyone, but it wasn't a big deal for me.
What I did was recreate the "configuration file". A step by step is listed below in case anyone else needs to do it. For the record, DW CS4 was the program causing me grief. (I also run CS6 and it was fine, as well as DW8 for really old sites)
1: Navigate to the APPDATA folder and rename "Configuration" to "_Configuration".
In Windows 7 this is "C:\users\<USERHERE>\AppData\Roaming\Adobe\Dreamweaver CS4\en_US\
2: Start Dreamweaver CS4 (this recreated the Configuration Folder)
3: Close Dreamweaver, and open the DW4 extension manager
4: Remove all plug ins within the list (they won't load or work anyway)
5: Reload all of your plugins (I keep mine really organized, so it only took a few minutes)
6: Restart Dreamweaver and enter your WA serial numbers as needed.
Everything is working 100% - and I am no longer receiving the error message. I have restarted DW_CS4 at least 25 times, and it would have triggered that message more than a few times by now.
By keeping the old configuration file (_configuration) I am able to retrieve old snippets and custom code I may have changed within it.