As I have different _config files for my MVC project I need to be able to sync via ftp and exclude certain files.
Q: Is it possible to indicate which files you want to sync via ftp as apposed to all as it now seems to be?

Thank you
Jonathan

You can set an allow and disallow filter for publishing (applies to synchronizing too). Open your Project Properties, and then click the Properties button to the right of the Root Directory entry. The rest should make sense

Not part of your question, but possibly helpful: I have not been able to achieve reliable synchronization using FTP -- date comparisons across different time zones are problematic. However, SFTP has been working like a charm

I'd recommend to tune NTP service on the server and Windows Time on your development machine, also don't forget to enter correct time offset in the account settings. Then upload a new file and check its date/time stamp in the PhpED's Explorer window. It should be very close to current time on your machine.