ibus-1.3.7 works incorrectly with m17n. The same problem at debian: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=593315 My version of ibus-m17n is 1.3.0. When I copied ibus-engine-m17n from deb to my system, all works fine.
I confirm this, cannot activate Japanese Anthy input after updating ibus-m17n to 1.3.1
Sorry, my problem wasn't related - solved it my deleteing ibus files from ~/
Fixed in 1.3.1