When I first got my RR Eco-Mesh shirt, the fabric felt so scratchy on me that I almost returned it. I thought it would result in chafing. I kept it and have since either gotten used to the fabric, or the fabric softened up - I don't know which.
If the chafing is caused by a seam, it's obviously a bad design and not the fabric. I recently got the Eco-Mesh pants and fell in love instantly. They are geared more towards warm weather pursuits, but try a pair on if you get a chance. The thing that impressed me was the feeling like there weren't any seams at all. It was like wearing silk! They are very thin but amazingly tough - their maiden voyage was through 9 hours of slot canyon in Southern Utah getting scraped against sandstone walls. They didn't show any signs of wear despite the solid abuse. And when RailRiders says "quick-dry fabric", boy do they mean it!
So... I guess my suggestion is throw the pants in the wash a couple times or just take them on a few more hikes and see what happens. If they still don't work for you, it would be a good chance to see what RR's customer service is like.