I'm basing the information off Yamaha's website. If you go to their website here:
http://www.yamaha-motor.com/sport/products/modelspecs/6/0/specs.aspx
Then on the "compare" pull down, select the 2005 R1 and also the 2006 R1. It should show you the specs I am referencing.
The manuals on line which you can download for the 2004 show the specs which match the 2006 bike, not the 2004/2005 bikes. The only other answer is that the specs on the Yamaha website are incorrect.
However, if you key off the compression ratio, it does make sense that the ratio would be lower in 2004/2005 and then bumped up slightly in 2006 - or at least it seems like it would make sense.
When I have a minute, I'll see if I can cross-reference the publication numbers in the PDF files with Yamaha or the dealer or something.
As it stands right now, I have merged all the 2004-2006 information into a single zip file and renamed the service manual to 2006 (from 2004/2005) to match what I see on Yamaha's website with regard to the 2006 vs 2004/5 specs.
That's the latest info I have to go on right now.
Ray