WebMatrix2 published my apps successfully. When upgrading to WebMatrix3, the apps with no db connection could be published, but the apps with db connection encountered a problem. After I inputed the connection string at publish setting dialog and saved & reopened the dialog, the connection string setting always lost. The connection string I inputed just disappeared, other settings remained. the app could not be published again.
I thinked maybe because I had changed the "My Documents" default path to disk d, WebMatrix3 had a problem to read the encrypted connection string value in D:\user\Documents\IISExpress\config\Web Deploy\Site1\lastValuesUsed.xml.
I rebooted my pc, reinstalled WebMatrix3, replaced IISExpress8 to IISExpress7.5, the problem still occurs. It bothered me several days.
Before I prepared to reinstall my windows7, I found the WebMatrix2 link http://www.microsoft.com/web/handlers/webpi.ashx?command=getinstallerredirect&appid=WebMatrix2ForVistaOrBelow.
After I backed to WebMatrix2, I found the connection string saved and the app published successfully again. All is well.