Your answer why is pretty simple if you think about it. The reason the "dots of the fabric", or the "grain", or whatever you want to call it, are different sizes on the upper and lower templates is the exact same reason it took you so long to figure out how to match lines across the seams. The applicable template sections are themselves are different sizes from each other.
On a 512x512 canvas, the back section of the upper template is 199 pixels across at the waist (not counting the bleed), while the back section of the lower is only 175 pixels across. For the front, it's 218 and 197, for the top and bottom, respectively. That means your fabric grain has to be about 14% larger on the bottom than on the top for it to match up in the front, and about 10% larger for it to match in the back.
That's the why, which as I said is pretty simple. The how, on the other hand, for fixing it, is considerably more complicated. As I just said, you need to increase the size of the grain at the waist on the lower template for the fabric to match from top to bottom. That increase isn't so neat and uniform though, as the number I just posted might suggest.
It's not even just a question of finding the right ratio by which to increase or decrease the grain size for each section as a whole. Every single UV face has its own ratio compared to its mate across each seam. For example, on the front lower, the first face at the upper left hand corner is 24 pixels across. The matching face on the front upper is only 8 pixels across, or 3 times smaller. And that's just one UV face out of the 56 you need to deal with for the waist alone! There are hundreds of UV faces at the seams when you add them all up, all the way around all sections, and no two are the same size.
To get any kind of grain to match across all seams at all points is very time-consuming process. You literally need to make sure every single grain is accounted for, and resized appropriately as it crosses the border. A simpler solution is to avoid using highly grained fabrics in the first place, but if that's not an option, then you have a lot of work to do. There's no way around that.
I'd highly recommend you start using Robin's and/or Chip's templates, by the way, if you're not already. They're a lot more detailed than the Linden ones, and they both come with guides to help you match things across seams. Just remember to downsize your outputted TGA's to 512x512 before you upload to SL, since those templates are 1024x1024.
Welcome to the world of crappy UV mapping. As much as I respect and admire all the Lindens, I have to say, whomever it was they hired to create the UV's on the avatar model must have been a crack-smoking, absinthe-drinking, schizophrenic, mentally retarded, half blind, one-armed circus freak, or at least someone doing a fair impression of one that day.
