I saw this problem with the last couple of sets of boards I ordered so I decided to track it down.
It turns out that if you have a throughhole component with a square pad on top and a round pad underneath that the round pad doesn't get updated according to design rules even though that is checked in the pad properties.
I was using the DIP8300 and DIP14300 footprints from the master database and I set up PCB design rules to set the annular ring to 100% of drill-radius so I could actually see some pad to solder to. This works perfectly for all the pins except pin 1 and it even works there on the top layer. If you go in and manually select that pad and look at the copper bottom layer, you can see that the annular ring hasn't been resized though. If you change the shape to square or rounded square and change it back to round, it updates from the design rules properly.
This is in v.11. Not sure if this problem is still there in 12 ...
Mike
