Hey,
Recently I had a problem with SyncToy 2.0 (new ver) not running either of my folder pairs, which previously worked not only in ver 1, but the Beta ver 2. I'd gone thru installed apps and uninstalled VB 2005 Express Edition and it (or me.....) uninstalled SQL and SyncToy depends on that. I reran the install app for SyncToy 2.0 and selected Repair and it worked.
So if SyncToy does not work and it has worked before, rerun setup and select Repair. My problem was uninstalling something it depended on, so I got it working again with no probs.
Hope this helps somebody!!!!
Ted