When configuring Merge Replication for Web Synchronization it's common to encounter the error The Proxy Auto-configuration URL was not found and for replication to fail on synchronization.  This error occurs when either the certificate is not installed properly, and/or Internet Explorer proxy settings are set.

To alleviate this issue, verify the certificate is installed properly at the subscriber(s) for the merge agent process account.  Then, open Internet Explorer, go to Internet Options -> Connections tab -> LAN settings, and uncheck Automatically detect settings.