After reading your comments regarding the pixel offset of the 'M' in the startup screen of Mac OS 8.6, I just had to see for myself.
I opened up ResEdit and opened the System file, went hunting for the 'pict' resource, and then found the full-size color startup screen image.
This is normal. I know what you're going to say, "how can that be normal? the letters aren't even along the bottom!"
This has to do with typography. Look at any Apple poster, particularly any poster with the "Think different." slogan on it. Also of particular not should be the 5 flavor iMac poster which says "Yum."
In typography, there is what is known as a baseline. The baseline is what all the characters "sit" on. There's a catch, though. Any character which has a curved bottom (as all the letters & numbers except the 'M' in Mac OS 8.6 do), the bottom curve of those characters will extend very slightly below the baseline.
If you look closely at the "Think different." slogan, you'll see that the 'd' and the two 'e's in "different" have their curves descending just a little below the rest of the letters. The same goes for the 'u' on the iMac "Yum." poster.
Of course, this greatly depends on the font being used; some fonts do not behave this way. But, Apple uses a custom-made font, called Apple Garamond (a variation on Garamond), and it was a conscious decision when designing this font to maintain this standard typographical practice.
For a very easy-to-get-to example, just surf on over to http://www.apple.com/ and look at all the text written in Apple Garamond, including the word "Apple" itself. You'll see the same behavior.
I also looked at the box that Mac OS 8.0 came in. It, too, shows the bottom of the 'M' slightly above the bottoms of the rest fo the letters. You have to remember that this is on purpose, and that it's something of an optical illusion. It's not the 'M' that's too far up, it's the other letters that are (correctly) sneaking down just a bit. If the 'M' were at the same level as the rest of the letters, it just wouldn't look right.
For an example of this visual trick in another font, simply go look at the logo at the top of the main MacNN page. The words "Macintosh News Network" show this behavior very nicely.
To sum up, no this isn't some big government/alien/Microsoft conspiracy to make your new Mac OS 8.6 startup screen look wrong. It's exactly as it should be.
I hope this helps. =)