When I am building my rig from a template, there are values on the arms and legs on the rotation transforms. (Both FK and IK)
all the other controls are zeroed out.
what might be causing this?
When I do “Zero” on the controls the arms go into “T” pose instead of the “A” pose they were rigged at. Like the controls want to default to “T” after its built
This is by design. Some controls have a different rest pose and bind pose.
In the case of the arm IK is to align with the world space. So when you animate the representation on the grapheditor of each axis is initially match to the world and not tilt based on the model pose 
Ah, gotcha.
Is there a way to “zero out” the controls after the rig is built?
custom step are your friend
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Thank you 