How do I move between windows in IRSSI?

Finally worked this out. The alt+number conflicts with gnome-terminal's keyboard shortcuts to switch between tabs. That was always the case, but in older versions of gnome-terminal the combo would switch tabs if there were tabs to switch to and switch IRSSI windows if there weren't.

If you disable or re-map the "Switch to Tab ..." shortcuts (at Terminal > Preferences > Shortcuts) you can use alt2 in IRSSI again.

Double-click on the shortcut key and you'll see "New accelerator..." -- from there Backspace will disable the shortcut, or you can create a new shortcut. I used ctrlalt2.

You can also use the commands /1, /2, ... /N, which is what I like to do.