I ran into the same issue on a half century with my mountain bike last month. The local shop guys had no real answer. I'm thinking vertical bar ends would at least let me shift positions for long stretches. I chalked it up to the ergonomics of a mountain bike not being proper for long distance highway riding. I've never run into the problem in urban or off-road riding, probably because my hands are moving around a lot.
Also, I agree padding may be making it worse. It's the same issue with saddles--a puffy padded seat is actually far less comfortable on long rides than a Brooks.