I am traveling in my minecart on a track.The tunnels walls, roof and floor are one block thick and the tunnel is 2 blocks high.I press shift by mistake and i fell trough the floor into the void. I don't know the cause of it but it doesn't do it when it's a 3 block high tunnel.
I cannot reproduce in 1.9-pre2. Made a tunnel like you specified and I didn't fall through.