one way to "fix" the misalignment is to create a glyph for the panel and align it over the screwup.
If that works with the design and depending on where the issue is visible. 
Like V says...a sizing margin set to the exact edge of a sqare will allow it to tile from that edge and look fine(like your brushed aluminum bottom edge)...the right side is where you will encounter oddities because Start menus dont expand and shrink in even increments(especially XP's)because of the dividers between the sections.(and different size icons)
In Vista you might get lucky (because I think it only uses 1 size icons right?)if you set the amount of pixels tiled to exactly what it grows or shrinks when programs are added or taken away.(which means the texture has to be made for that exact size) Again,its the dividers that are likely to give you fits because the mess up the calculation...trial and error man...mostly error. 
XP is much tougher I think because of the different ways it can be configured.
Hope that makes sense...brain good not work all time. 
With Neutronium DM I wanted the texture bad enough that I just ignored the odd occasional alignment.It only showed some of the time and was just a single doubled line of pixels.It was a compromise and they always suck. 
I figure most people don't resize their Start Menus.
Sorry...they do...a lot.
Just less with Vista because it starts out so frickin huge anyways.
