When publishing using the FTP protocol, WebMatrix by default keeps track of files that are changed on the local computer. This makes all FTP transfers after the first transfer faster because WebMatrix does not need to obtain a folder list from the remote server to determine what files are different.
There are two resolutions available:
1) (Recommended) Clear the cached list of changed files
a. Close WebMatrix
b. Open the IIS Express configuration directory in Explorer: %USERPROFILE%\IISExpress\config\PublishUI
c. Open the folder named after your site. For example, if your site is named Bakery, open the bakery folder.
e. Delete the CSV file in this folder
f. Open WebMatrix and try publishing again
2) Disable the featurea. Open WebMatrix
b. Click the Application Menu in the top-left corner of the window
c. Click Options
d. Click Publishing
e. Uncheck “Make FTP faster by only publishing the files that have changed on this computer”
Note: This will make FTP transfers significantly slower