It's very common for derailleur hangers to get bent during shipping while the bike is in the box. If there's any sizable impact on the right side of the box the derailleur and hanger seem to get pushed in a bit.
Not with reference to your current problem, but to give you a heads up about using Paul's Thumbies: it's not uncommon for the screw that holds down the right side shifter to work loose. This causes poor shifting (acts just like cable drag due to slop at the shifter) and can damage the Thumbie at the mount. I put Pauls Thumbies on my girlfriend's touring bike and had this happen a year later (unfortunately, she has a high tolerance for a poor shifting bike, and didn't make me aware of the problem for quite a while which is how I know that this can damage the Thumbie). The fix for this is to either use Locktite Blue on assembly, or if you want to make really certain that it doesn't come loose, use a longer shifter mounting bold and put a locknut on the underside of the Thumbie, which is what we did.