I don't (usually) wear bike shorts, so take everything I have to say with a grain of salt.

I've heard good things from my fellow padded shorts hating people around here about tri shorts- still a chamois, but no padding. If both of your pairs of bike shorts are padded, this might be worth a try.

Second, all of the things people have said above about time in the saddle, riding positions, stops, etc. probably have at least some bearing on your experience, even if you do have the wrong shorts for you. I could even see it being something to do with how hard you're working for those 20 miles.

Finally, even though you probably can't ride 300 miles in jeans, I just wanted to share for everyone reading that some people really do prefer to ride in jeans, and find it comfortable. My SO's "cylcing shorts" are a pair of knee length denim shorts. To each their own, I suppose.