Yeah, a different pair of cycling shorts can make a difference. Different ones fit differently. Basic Performance shorts fit me great--no such problems ever. Basic Nashbar shorts, not as well, and I get rubbed the wrong way, and have to constantly readjust myself. This only means that in my case, Performance shorts fit me better; someone else might discover the reverse results. I don't buy fancier shorts, so I dunno for anything else.
In short, try a different brand of shorts, try some kind of goop (never have used them myself, but some people find goop to be great stuff).