When you set a transform object for several bones at the same time.
# Get control
transform_control = animation_clip.GetControl("Layer", bone1)
# Set transform bone 1
transform_control.SetValue(RLPy.RTime(0), new_transform_object)

# Get control
transform_control = animation_clip.GetControl("Layer", bone2)
# Set transform bone 2
transform_control.SetValue(RLPy.RTime(0), new_transform_object)

# Get control
transform_control = animation_clip.GetControl("Layer", bone3)
# Set transform bone 3
transform_control.SetValue(RLPy.RTime(0), new_transform_object)

Only the last bone will be set (nr 3). The rest of the SetValue (for bone 1 and 2) are ignored.