if you are running them in STEREO , then you are probably just noticing the delay between the right and left channel. If you want them to be in sync, then you will need to bridge your amp and run a MONO channel for bass (this is very common)
if they sound a bit weak, then you may have the polarity of one sub backwards. If they are in the same enclosure , they will sound very weak if it's reversed. easiest way to test this is turn the balance to one side or disconnect one sub and see if your bass gets louder. if it does, then one is backwards.
