Firstly, Pathfinder' rules as written are such that positive bonuses of the same type applied to an ability/skill/etc. do not stack, and that only the highest bonus applies (negative ones always stack). The implications of this are what I'm questioning, when they affect things that are tied together.
The PC (let's call him Jimbo) is a Barbarian 1 / Cavalier 2 (Order of the Sword). Barbarians can rage, which grants Jimbo a +2 morale bonus to his strength and constitution ability modifiers. The Order of the Sword lets Jimbo add a morale bonus to attack rolls against the target of his challenge (here, it will be a +1).
Now, say that Jimbo is raging and has declared his challenge against a certain enemy. Because his attack modifier is affected by the morale bonus to his strength, is Jimbo unable to receive the +1 to his attack roll from his order's challenge ability?