How long (time wise) are you riding when you are in your jeans - yes the mileage may add up, but the continuous time on saddle may be quite short when you are riding around town and making lots of stops. When you are riding to train you are sitting on your saddle for long periods of time without stopping.

From your description, I'd look to the saddle rather than the shorts. It sounds like you are having pressure, rubbing issues that don't become apparent until you've been sitting on it for some time. You may need a different shape/size, cut-out, non-cut out. Any saddle can feel OK for short periods of time, but start to show its shortcomings when you ride longer.

I personally find jeans to be extremely uncomfortable... I had a really short trip to take a few days ago (about 5.5 - 6 miles round trip) so I just hopped on my bike and rolled up my pant leg... I didn't like it one little bit...