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.