no not necessarily always have to be in any hierachical order.

its a logical approach.

i dont rig in maya anymore unless i have to luckily


:beer:

i also got some similar issues on past rigs at work.

so instead of using the normal parenting in maya, i use more often the new parent constrain in the constrain menu. its like the constrain...

since you already toggled inherit transform on/off and the problem persists,
the only thing i can think of is to try to change transformation order on the geometry. maybe [*maybe] that might help....