Sometimes when I select the New Site entry it's on no encryption but the port is always 990. Changing the encryption to explicit does not change the port. But selecting explicit, then implicit and after that explicit again it correctly puts 21.
It is not 100% reproducible but I can't figure out what other factors come into play. Without fail the effect comes to bear when New Site on opening is initially (not manually) set to no encryption and you change to explicit.
Edit: As is so often the case, right after posting I got a chance of filming it (sorry for the phone video): https://www.youtube.com/watch?v=a12_2dQC_oM