The Slingbox only sends across remote control signals through IR. If the cable boxes were set to receive RF signals, the Slingbox would not be able to change channels at all. The only explanation for this issue would be that the IR signal that is being sent out from the Slingbox is reaching both cable boxes.
You're on the right track repositioning the other cable box in relation to the Slingbox. Some of the stranger cases of this happening that we've seen is when the cable boxes are in completely different rooms, but the IR signal from the Slingbox is actually bouncing off surfaces (mirrors, windows, reflective surfaces), and reaching the other cable box that way. I would try addressing that by closing a door, placing some kind of IR blocker or physical object near the other cable box...anything you might think of that can block that signal, and that can work with your individual setup.
Hope this helps! Let us know!