I did have had similar issues my my discs brakes but there was no going to V's especially on downhill tracks. I actually find them pretty low maintenance as long as you look after them. It's unusual both would be playing up at the same time.
On regular pavement you should not have any problems.
Firstly if you are constantly removing and remounting the wheels you need to make sure that they are in correct position all the way down in the bracket and spin the wheels to make sure they spin freely before tightening. A little bit misaligned they will rub.
They do clog with dust from the brakes or dirt etc.. you need to wipe down the discs, someone suggested brake disc cleaner for motobikes or just use a clean cloth and wipe them down. The often make a light rubbing sound due to minimal clearance and dust in the gap if it doesnt slow your wheels down you just ignore it or what I do is hold the brake levers down a bit and ride a little to let the brakes rub itself clear.
Rain/Water (this is where my problems started) disc brakes don't like getting wet, never hose or wash them it either puts fine dust or grit into the calipers/pistons and they can jam and not release.
Check to see when you pull the brake levers if the brake pads close onto the discs and release there should be some clearance or an obvious gap up to half a mm. If it doesnt show obvious release the pistons are probably jammed. I havent worked on the Hayes before but you should be able to download some servicing/instructions from their website.
Are the discs bent? If so they need to be replaced or flattened back out.
If there is obvious clearance between discs and pads the calipers may be misaligned.You will need to realign the caliper unit. I am not sure with the hayes if they will automatically align when mounting. what you can do is loosen the screws that hold the caliper to the frame mounts on your bike, enough to give the caliper free movement. then either with tape or rope hold the corresponding brake levers down to clamp the discs tightly. Then tighten the screws again while the discs are being clamped. Once completed undo the levers.
If all that doesnt work,
You can try remove the brake pads and clean around and under where they are clipped and around the piston (**DO NOT PULL THE LEVERS during this process and you can pop the pistons out and make it leak and put AIR in the hydraulic hose**) Put the pads back in and try putting the wheel back in. If you are lucky this might work. If not you may have to open them up and clean the inside. could be a messy job with fluid, seal, bleeding etc which you need a kit to do.
Send it too a bike shop..
Hope that helps,