Our setup is this - we have a drilled well and a dug well, both come into the house and have their own breaker switches, and both come through the same pressure tank in the basement. The dug well has a typical indoor water pump and the drilled well has a sunken pump.
At first we were puzzled because it seemed totally random, but as time goes by we've concluded that we lose our water pressure whenever there is a long, slow drain on the water - as in, if the toilet runs for several hours, when the water softener system runs through its flushing cycle, or when the dishwasher runs. By contrast, we can have a typical morning with two showers, washing dishes in the sink, and doing 2-3 loads of laundry, and have no problems whatsoever.
Have you heard of this kind of thing happening?