A web configuration modification operation is already running
This error occurs in Farm enviroment when you change web.config file in SharePoint via SPWebConfigModification when previously change isn’t synchronized over whole Farm (see "Save Only Once per Event or Feature Activation" in Mark Wagner article)
The second case happened when you run modification under Application pool with insuficcient rights which leads to DCOM errors in Event log (e.g. The application-specific permission settings do not grant Local Activation permission for the COM Server application with CLSID …) and in Central Admin>Operations>Job Definitions will stay hang timer job titled "Windows SharePoint Services Web.Config Update" which executes "One Time" and will have an "N/A" listed for the Web Application. This timer job block any further modification, but you can delete this job, set appropriate rights and run modification again.
References:
- Mark Wagner – How To: Modify the web.config file in SharePoint using SPWebConfigModification
http://www.crsw.com/mark/Lists/Posts/Post.aspx?ID=32 - David McWee – A web configuration modification operation is already running.
http://dmcwee.spaces.live.com/blog/cns!3434442F19CE5B65!135.entry