Hi,
I am not so sure about this solution.
In Web.Config File, if you take a look there will be two Files under the "Web.Config" category.
The sub Files of that Branch will be named as
1.Web.Debug.config
2.Web.Release.config
If you are Debugging the File, the Config details will be consumed from the File
.Web.Debug.config
and if you execute the File there is a chance to use the file from common Web.config or the other.
Please check the configure entries are fine and identitical.
Please confirm your observation, so we can help you in this. Also conform what type of Error you are facing or what functionality not working as expected. That will be helpfull for others to guide you.
Thanks!