but after that clicking on "New Session" or "Options > Preferences" will send the dialogue boxes (focused) behind the main window.
Only these two? Or all dialog boxes?
Do I understand right, this happens only after WinSCP reconnects after the PC resumed from sleep? And it never recovers, so you have to close WinSCP. Correct?
I believe you did not answer this:
If the first, what if you open another instance of WinSCP during those ~40 seconds and try to connect? Does it connect immediately or does it also take long?