Is that when you choose the 48K Mode from the 128K menu?
Or is it when selecting 48K Mode from the left thumb stick menu?
If it's the former then it is meant to be like that - the keyboard that is displayed is determined by the machine type selected (e.g. 48K, 128K, Plus 2). It isn't affected by any changes that go on internally in the spectrum software.
Think about it - if you are using a real 128K speccy and go into 48K mode - you don't suddenly get a 48K keyboard!

If it's the second one then there is something bizarre going on - there's no way that should happen!
Just to keep you guys posted - progress has been amazing in the last couple of weeks - I think you'll all be pleased with the new version when it's ready!

Carch