In reply to:

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Were these drives formatted with the builder image, or by hand

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The "fast" drive is the original drive from the factory and has never been reformatted or anything like that. So it is as it came from the factory.

The second drive was a brand new drive installed in the player and formatted using the disk builder. I followed the instructions word for word from the Drive Upgrade page on riocar.org.

The only thing that did happen was that when I put the new drive in, I put it in as a master and I put the original drive in as a slave in the hope that the newer drive might have been a little faster. I also copied the dynamic data from the old drive to the new drive and it worked perfectly in case anyone was wondering.

I know it's not going to affect things too much in real life but could 1k blocks instead of 4k blocks pose any sort of problem later on apart from slow fscks? Although I will try turning on the other swap instead and see how fast that goes...