Bike boxes are right on the border between two oversize classes. For FedEx and UPS, the rule is length + 2*width + 2*height < 130". Your box comes out to 129", so you or the person at the counter mismeasured, or he didn't measure it at all and just assumed it was extra oversize.

For example, go to UPS.com and do "Detailed Time and Cost." For a cross country trip, a 30 lb box that measures 51"x31"x8" is $80, but a box that measures 51"x32"x8" is $140. In order to get a decent price, you have to make absolutely sure that your box is under the limit, and that the clerk is not being sloppy.