the tardis flight mode isn't working for me it doesn't let me control my tardis, ill tell what I do.

1. I enter flight

2. it removes my tardis on outside

3. then it just my self and can play normally 

I can still summon the Tardis but then I try again but it does the same thing I don't know how to fix this annoying problem.

This is because the flight panel has been broken. Why would you even use the flight panel? The server clearly states not to use the flight panel

because I play in single player.

The flight panel is broken on SP too in U48 it will be fixed (I think).