Have you tried getting the discs skimmed?
It sounds like you have the classic symptons of pedal pulsation. If so, then the brake disc has either been worn away through friction with the pad or there is some pad material left on the disc (esp with automatics when the brake is always on when you stop and your discs are hot). The end result is instead of having a flat disc, you have one with DTV (disc thickness variation) with peaks and troughs instead of a flat surface (imagine a mountain range). When you apply the brakes pedal the pad is bouncing from peak to peak instead of having constant contact with the disc. This causes your brake pedal to jump.
Pedal pulsation is very noticable and usually only occurs at certain speeds (in your case 45-50mph) which is why I think that could be the problem. Visit www.skimmydiscs.co.uk to find your nearest lathe. There are some out there but make sure they have a black one called a PFM 9 - it compensates automatically for lateral run-out which be the cause of the problem and skims discs in 10 minutes. Make sure you know the manufacturer minimum thickness for your discs though as it's illegal to skim below this.
Whilst on brake skimming, think about getting your discs done when you have new pads fitted too. It costs a bit extra but at least you have 100% braking efficiency straight away instead of having bad brakes until they bed in 500 miles later.
It could be the wheel balance as well though - I have little faith in wheel balancing in shops mainly due to the people which carry out. Many shops i've been to can't balance a wheel to zero and are quite happy to put over 100 grams on which is diabolical. Do you know how much weight they put on your wheels?
Take your motor back to your wheel balancing man and ask him to put it back on the wheel balancer and see if it comes up zero - it won't !!!! If they "fix" the problem and get the zero read out, take the wheel off, rotate it 90 degrees and do it again - it won't come up zero twice. If it does then pay the man and take a business card because good wheel balancers are rare in the country.
Good luck, I hope you get it sorted soon