Eeeh, alot we don't know about evidently; and it was copied to Kibaki. Could have pointed to Raila wanting to really take action on corruption (for whatever motives). Or maybe Raila's frustration came because Ruto was effectively becoming a stranger and he could discipline/reclaim the post for his party.
Letter could have contributed to the lack of trust, and led perhaps the move done by Kibaki (without consultation) of stealing the thunder from Raila. And then Raila's relation (also without consultation). No one wanted the other to look too good...
But I wonder whether they had chatted about it earlier, and Kibaki in usual laissez-faire style was non-committal leading to Raila appealing elsewhere...
Everybody sees Raila's moves so can judge him for them. I've spoken to people who know, Kibaki even from 2002 campaign - always thought it more tricky when you've got a commodity with hidden actions.