Cannot input ちゃ (cya) on ubuntu
ちゃ is "cha," not "cya" if you want "kya" then you'd use きゃ.
You can see the Wikipedia article ローマ字入力 better implement the requirements (Obsolete on JIS) of the input in the Roman alphabet. However, in many cases seems to be proper keystroke.
https://bugs.launchpad.net/ubuntu/+source/ibus/+bug/603111
This is in Ubuntu 10.04. Not sure where the problem came from. From anthy or when packaging with ubuntu.