If you are wearing one of the new faction tabards (e.g. Thunder Bluff, Stormwind, Orgrimmar, Ironforge, etc.), you will only receive reputation gains for that city/faction when in Classic (1-60), Northrend (70-80), and Cataclysm (80-85) dungeons. Outland dungeons will not currently provide reputation gains for the "home city" faction you are championing; this is intended.
Yeah, I'm kind of curious myself. Why is that?
Most burning crusade dungeons already award rep to one faction or another. It was probably thought it it would be unbalanced if you where earning rep for 2 factions at once, or it was too difficult for Blizzard to work out the interactions between the tabard and regular reputation gain at this time.
Edit: G*d-damn the General forums get alot of traffic; by the time I had this typed out 4 other posts had beaten me to saying the same thing.