The photo with the long bolts sticking out appears to show that one mount was brazed a degree or two away from square to the center line. Must be tricky to get that right.

Me, I get satisfaction out of correcting tiny, easily resolved problems like this one. I'd just disassemble the lever, clamp the barrel in a vise, and give the lever a couple of light taps with a hammer or use a metal tube (such as a seatpost) to bend it a bit. If your bike had been sold by a bike shop, chances are that that's what an experienced mechanic would have done during the assembly.

(Though I've known some anal-retentive mechanics who would have insisted on sending the bike back to Trek or whoever. One guy in a shop I managed insisted that a Marinoni frame we'd imported from the factory in Canada had been built out of alignment. I arranged to have it sent back to the factory on their dime. They checked it. It was perfect. They cancelled our account. Then I found out that that was the first frame that the mechanic had ever checked for alignment.)

But if you want to follow up with Bikes Direct, do an end run around the lower-level employees. The CEO is Mike Spratt (mikespratt@bikesdirect.com).