The reason for this behavior is that by default the RadEdiotr for MOSS uses the embedded in the RadEditor.Net2.dll resources. This is why you see difference between the loaded file and the one on the disc.
Here is what you can do.
1. You can set the UseEmbeddedScripts property to false. In order to do this modify the respective ConfixFile.xml and ListConfigFile.xml, which are located in the Program Files/Common Files/Microsoft Shared/web server extensions/wpresources/RadEditorSharePoint/4.x.x.x__1f131a624888eeed/RadControls/Editor folder. Add the following code.
2. Make sure that you have the correct dll files in the GAC. You can rename the RadEditorMOSS.wsp to RadEditorMOSS.cap and extract the files in it by any archiving program. There you can find RadEditor.Net2.dll and RadEditorSharePoint.dll. Just replace the current dlls in the GAC with the once from the wsp file.
I hope this helps.
All the best,
the Telerik team