When you got the bike fit did you explain to the fitter about your problems? I'm assuming you mean the female groin area, the pubic bone etc. If only after an hour you have pain something is really wrong. I usually get pain but after 3 - 4 hours of riding. Make sure you are wearing properly fitted bike shorts with a good chamois, wear no underwear or liners go "commando to prevent irritation and chafing. Get a 6 panel + short (8 panel is best). 4 panel shorts sometimes have seams that can irritate. Make sure you have the proper saddle for you. If you are chafing inside your legs, then the saddle maybe too wide. Get one narrower and not as "cushy." A saddle with a female specific cut-out might help. Make sure you are properly positioned on the saddle (not too forward or too far back).

Note, most of us get sore down there. You need to make sure you are giving yourself a break and lift out of the saddle now and then. Unfortunately it's just a hazard of cycling.