the rolling diameter of the 06 civic sport tyres (205/55R16) is 632mm, the 07 (215/45R17) is 625mm which is about a 1% difference, or 0.8kph at 80kph. sounds like ur problem is much bigger than that...
it isn't the first time i've heard of this problem, there was another thread where someone was driving alongside his mate's civic, and from looking at the speedos of both found that they were reading very differently...
just hassle honda again about it, it might take them a few goes but they'll probably be able to fix it in the end