Calibration Help-Questions.

Hey gang,
I finally got my SD2 dialed in and calibrated then I had to move it and start using a new spool of filament so I'm dialing it in again. What fun!:)  My situation is this.
i'm printing  http://www.thingiverse.com/thing:252490 and it's to be 110 x & Y long and the towers and holes are to be 5 and 10.  When I measure it my lengths are a little shy, 109.90-109.85 but my towers are too big 5.8, 10.2. 

Why/how can I be too short when measuring the whole length but be too wide on the towers? Shouldn't it either be too short or too wide along the lengths as well as the towers? How can x be giving me too much x in one area and not enough in the other?

In general I've been sticking to the longer (but too short) measurements for my math. I just don't want to keep wasting filament chasing 2 sets of contradicting numbers. Any help or info anyone could offer is much appreciated. Thanks.