In order to close a popped up sunroof, you typically just push the button completely forward (towards the windshield). On one occasion, I found that it was not behaving (closes then re-opens) and I believe it was because I had the vehicle off while fussing with it in my driveway... all of a sudden the controls seemed to vary.

Try with it on. And what do you mean closed on one side... front vs. back popup? or left vs. right side on both glasses? Odd that it's even possible if it's the latter.

__________________
'08 X5 3.0si - Alpine White / Saddle Brown interior
Specs: Sport Pkg, Premium Pkg, Tech Pkg, Comfort Access, Aero Kit, Style 433 staggered 20s on Conti DWS
Mods: Carbon 35 tint, LED angel eyes, GP Thunder 7500k fogs, H&R 20mm/25mm spacers, clear reflectors, gunsmoke-tinted taillights
Coded: Digital speedo, windows/sunroof/tailgate close via keyfob

X5 pics at Flickr