iPad update 5.1, different connection, different size of update
It sounds like you're talking about the difference between an "Over The Air" (OTA) update, also called a delta update, done by tapping a button in the device's Settings - and a normal update done by clicking "Update" in iTunes on your computer.

OTA updates are smaller because they only include the new assets (code, images, etc.) from the update, instead of replacing all the assets on the device.

This article includes an example of this difference on an iPhone 4:


  Not only are over-the-air updates simple to install, but they’re also deltas. That means that the updates contain only the minimum data needed to upgrade, instead of the complete operating system. For the 5.0.1 update for a GSM iPhone 4, the over-the-air update weighed in at 44.6MB; the full download via iTunes was 790.7MB.