new tires, alignment marks
Yep, that's what those marks are. There are many reasons why they don't get lined up. The main reasons are being in a hurry, being lazy, not knowing better, just not caring, and tires that are difficult to mount. The "lower profile" the tire is, and the larger the rim diameter, the harder they are to mount, and easier it is to rip the bead. Remember "the tire guy" is usually the lowest paid and least experienced employee in the shop.
All of that being said, a good "straight" wheel and a quality modern tire should balance with minimal weight, like less then an ounce per side, on a modern tire balancer in calibration. Another thing to remember is that all metal valve stems and even the rubber stems with the chrome sleeve and chrome metal cap on them were never factored in to that equation as to where the "dot" got painted.
To really get the "least weight" on each wheel, the tire needs to be mounted 5 times, moving the dot 90 degrees each time, spin it on the balancer each time, then final mount the tire where it called for the least weight, irregardless of where the dot is, VERY FEW people want to pay for this.
Tipping your tire guy BEFORE he starts on your tires works wonders to get a quality job, it can also "buy you a ticket" watch, which is a good idea too.
TopHat