I have a 2007 and my passenger window runs slow up and does not completely close most times. The rear right passenger window goes down when top goes down but then goes up half way. It will go back down when I lower it individually with the power button. Could it be some sort of modulator, a fuse or the battery?

 

not a fuse or the battery. did you check to make sure nothing is binding (ie weather seals)? sounds like you are talking about the quarter glass not the door window? You may have an issue with the window regulator (google PN 31253534) but for models where the windows automatically operate (ie like my VW CC drops the windows 1/2 inch when the door open/close) there is programming involved that may require a reset if you recently had to disconnect the battery or you may need to call the dealer about a software update.