not as loud when car is moving

2 Alpine Type R 1042D subs, 1 Alpine PDX 1.1000 amp, Alpine CDE-9881 H/U, 2008 Pontiac G6 GT sedan. Is it possible for the subs to lose power when I drive the car or is it just my ears playing tricks on me. When I'm parked with the car running it sounds great but when I'm driving it seems to lose some power?

Does it get softer the faster you go?  That's because the car is moving forward, away from the bass.  Your subs are behind you so as you move down the street you leave the bass waves behind.  These are called "standing waves."  Try driving in reverse and see if it gets louder as you drive through the waves.

( the above is meant as satire...)

doppler effect?^^

i figure its just the road noise taking away from the bass

The boominess you hear may be because of enclosure size, but the sound changing with windows going up or down is normal, since the inside of your vehicle is part of the subwoofer system.  Sometimes it gets louder, sometimes it gets softer.  That's why the science of building a proper system must include the characteristics of the vehicle you're using, especially if your goal is maximum SPL.  And I hear that question all the time.