As I hinted, you can (almost) rule out the prop valve if your brake light is hooked up and not coming on when you have the problem. At least that tells you that the pressure is balanced between the front and rear. The light though only tells you balance, there could still be something wrong with the proportioning or metering valves in the prop valve.
If the valve is working correctly, the rear brakes should engage first before the front, though just barely. This assumes the rear brakes are installed correctly and adjusted. Here is a good article how the system works:
http://auto.howstuffworks.com/auto-parts/brakes/brake-types/master-brake2.htm The front disc has more stopping power than the rear pads though, so it is possible that the rear pads are also grabbing, it's just the front is where the problem is. If that is the case, then yes there's something wrong at the mc/booster or even at the brake pedal.
Just to keep things back to basics, you are using dot 3/4 fluid? Did you properly lube the caliper pins? Are you using metallic or ceramic front pads (I would not use organic for front brakes)?
I just searched google, two tips to try: check for pressure in the master cylinder by taking the cover off when the disks are locked up. Another thing to check is disconnecting the vacuum to the booster to see if that is causing the issue. (I don't suspect these tests but they are simple tests)