Hello! First let me let you know that this is still the best file transfer application I've come across yet. Thank you for all your hard work!
Since you've only recently incorporated FTP (can't say how happy I am that you've made that decision), it's only normal that not everything can be perfectly integrated within first few revisions. As a heavy user of the feature I only feel it's my duty to make some suggestions and reports in return.
One of my clients recently provided me an FTP server with 2-minute inactivity timeout. I have no idea why on earth would they do that, since it's not even public and I don't intend to keep 100 connections open all day long, but they're not the first one to enforce such useless and annoying limitation. I miss the keepalive features found in most FTP clients. Would love to see this implemented in WinSCP.
Even without keepalive, though, I see no reason why a modal dialog should pop up every time I'm disconnected, and freeze all my background connections and, when I refuse to reconnect, cancel them! (Background connections are totally unrelated to the primary, 'browsing' connection, no?) Even while reconnecting, the whole application becomes sluggish and freezes up!
A more reasonable behavior would be to have a little prompt in the status bar informing me that I've been cut off, while my background transfers remain undisturbed, and, if I try to continue browsing, silently reconnect for me in the background.
I don't know if I'm asking too much, but I hope you find my two cents useful. Thanks again.