As Tim said, this sounds normal; rsync will know that it's got a file that seems to be a partial copy of the remote file, but it still has to check that the file it has is in fact the file you're copying from.
As it's doing this check, it will show the number of bytes of the file it has "transferred", so it will look as though it's copying the file again - but if you look at the speed of the transfer, it should be much faster than would be possible across the network. Eventually rsync will get past the bytes it's already copied and find new bytes that need to be transferred across the network, and then you'll see the speed slow down.
In short, I think you're being confused by rsync's output, as it doesn't differentiate between "bytes transferred across the network" and "bytes transferred simply by checking that the local copy matches the remote copy"