The channel numbers are set by your cable provider -- it may be different from your set top box because most set top boxes are digital and use a totally different technology where numbers are programmed by software instead of by their carrier frequency.
In short, you can't really do anything about it. That's like our HDTV gets our PBS channel 22 on channel like 68.11 or something. You can either live with it or get a set top box from your cable company. We wrote out an index card with the channel numbers in the order we want them so we just look it up that way.