What you're experiencing sounds similar to a UTI, but luckily, yours isn't lasting. I would talk to your doctor about it, maybe even do some research to find a physician who cycles.

Do try changing your seat and getting a professional fit on your bike and don't be afraid to ask about the problem at your LBS. I know that can be um, uncomfortable, but the guys at my shop have no qualms talking to whomever about whatever problem and they'd never repeat it. ...Of course I work there, too, so it's a little different and I don't know if I'd willingly waltze into another shop and ask that question...
Specialized just came out with a "revolutionary" men's specific saddle that significantly improves penile blood loss while riding and they're currently working on making a women's saddle that performs a similar function. (I've spoken with the rep, he's promised me that they're doing all they can.) Something to look forward to in the future I guess...
By the way, that saddle is hideous. It's the most phallic thing I've ever seen. My boyfriend thinks it's comfy, but he won't be caught dead with it on his bike.

Hope you get things worked out. Don't let that continue. That's the most important thing.

a.f.