Pairing a remote RF doesn't disable the IR sensor on the box itself so that should still be operational. I'd guess the code you picked isn't the proper one for the Sling sensor. When I still had mine hooked up to my X1 box I had to use the remote code for the older legacy style platinum colored Cisco remotes.
Please let me know if you solve this I am on the verge of dumping my slingbox entirely because of this issue. Basically it is looking like if you upgrade your cable box sling technology will no longer work!