when you say you are running the latest flotilla software, you mean https://github.com/pimoroni/flotilla-pre (codenamed 'shipshape'), the one provided for PC, with the dock directly connected to that machine? or are you accessing the server running on a Pi over the network from your PC?
regardless, currently, the keyboard input are not always registered until you press a key on the keyboard, so make sure you press a key to force the input menu to update!