Anyway, the title says it all: it would be nice if the files that will be transfered because of a synchronisation can be added to the background queue ("Transfer on background by default" doesn't do it). That way there's a better oversight of the files that will be transfered, plus you can continue using the same instance of WinSCP.
Other than that I am totally in love with it ;). Just came across it and it's an awesome program. Thanks!