I have the same issue. Remote does not do anything on the (VR46A) Receiver side.
And yes, I plugged the IR cable into the IR port on the VT46A (Sender) and have the IR Emitter on cable box. The remote works perfectly (on my Comcast cable box) at the Sender side, but will not work on any (ABCD) channel on the Receiver side.
*************************************** UPDATE *******************************************
OK, problem solved just by messing with a lot more. Originally I had just stuck the IR Emitter to the front of the Motorola cable box. But for grinnies I took a flashlight and found precisely where the IR "electric eye" was located on the cable box and stuck it Right There. Though not perfect, its working! Just have to keep messing with it apparently.
Hope this helps someone out there.