Keep in mind that when your car is on, there are (at minimum) DRL'* assuming they haven't been disabled, your stereo (possibly), BCM'* and any other device required for the car to run. If there is a problem with a motor or the window is binding and the motor is working harder than normal, current draw will be higher. The reason I asked about windows individually was to determine if they all operate with about the same speed and don't seem to cause any undue draw. If one seems problematic, it may be with that particular component and not your electrical system.
The more likely suspects include your battery, alternator or poor cable connections. Any one of these (or a combination) can reduce the available current to supply required power to your car. Power windows are a fairly high current device.
StingRay Bike w/cards in the spokes, Weeeeeee!