I don't know exactly how you hooked it up, but the following from the Kohler install instructions may be pertinent:
"When diverting between the showerhead and handshower:showerhead. Default flow is through this port.
The small port is for the handshower.
The port directly across from the small port is for the
Do not install spouts with flow restrictors or handheld shower
units on the large (5/8² OD) bath outlet."
As I read your post, it sounds like you have connected the handheld to the larger ( default ) port, and they are saying this won't work that way.