The only way one can control multiple cable boxes using a Slingbox is if the IR (infrared) signal coming from the Slingbox and/or its IR cable is actually reaching both cable boxes. The reason it's happening with the Slingbox and not with the physical Comcast remote is because when you use that physical remote, the signal comes from the remote, not the Slingbox.
The only way to address this issue is to find a way to keep the IR signal coming from the Slingbox and its IR cable from reaching the cable box you do not want it to control. I would recommend either finding a way to re-position the Slingbox and the living room cable box in a way that the two devices do not "see" each other, or placing some physical object or IR blocker in between the two.
As far as the Slingbox updating goes, there isn't a way to change the time the Slingbox updates, but there may be a way you can work around it. You could try routing the HDMI cable from the cable box straight to the TV, and have component cables (red, blue, and green video cables with red and white audio cables) going from the cable box to the TV. Just a quick side note: If you do hook up the cables this way, you might run into copy protection in your cable box that shuts off the video signal to your Slingbox until you hook everything back up the way it was before. Can't hurt to try though, and if it works, it'll eliminate the interruption from the Slingbox update.
Hope this helps!