Just get rid of the popups
It's pointless to have a popup saying 'will reconnect in X seconds.' Just reconnect, with an indication in the status bar, and don't bother the user about it.
My only issue with WinSCP is the incessant popups. I frequently get one that says it couldn't copy the file for some reason. What's especially bad is it usually sits there under some other window while I'm trying to figure out why the file I thought I uploaded doesn't appear to be working.
Instead of warning about timeouts, warn about exceeding a threshold on the number of retries.
My only issue with WinSCP is the incessant popups. I frequently get one that says it couldn't copy the file for some reason. What's especially bad is it usually sits there under some other window while I'm trying to figure out why the file I thought I uploaded doesn't appear to be working.
Instead of warning about timeouts, warn about exceeding a threshold on the number of retries.