Some history on this may help. In March 2009 the Magic had a cruise with tons of 11 GTY staterooms at super prices. They paid no attention to linked ressies and just put people all over the ship. Guests were going on line to trade cabins with other guests, asking at GS to be swapped, etc. It was a huge mess.
May 2009, again a cruise with over 100 cabins booked at the 11 gty rate, but this time they DID put families either next to each other or very close to each other. We were in that bunch and were next to each other.
Most recently, it seems that if you book a regular GTY rate (as in a number with GTY), they make an effort to put you near each other if not next to each other. These rooms are assigned before the restricted IGT/OGT/VGT rates. If you booked a restricted fare, they still seem to be trying to place linked ressies near each other, but realize that you are in the last cabins assigned and they have limited locations to deal with. The more empty the ship, the more likely you are to be near your linked buddies.