I did a little research online and found that there are quite a few message boards that address this problem, which seems to be fairly common. The warping could also occur if you leave the mat in a hot car or keep it on a table that gets direct sunlight, so be careful with your cutting mats!
The first suggestion I tried was to put it between my mattress and the slats on my bedframe for a couple weeks, which made no difference at all.
The second was to soften the mat in a tub of warm water and then flatten it under a mountain of heavy books, which seemed to work! But a couple hours later the ripples were back.
I think the best idea I've seen is to salvage any usable parts of the mat by cutting it down and getting rid of the warped pieces, so I will try that next. Then I'm off to the craft store to get myself a new one!