It actually IS bugged, yet the OP is the only one that has even made a bug report about it. (EDIT: More detailed report https://www.warmane.com/bugtracker/report/34212)
The following information is from wowpedia and is how it should work: (http://wow.gamepedia.com/Championing)
The following tables outline the amount of reputation that may be earned toward a faction during a full clear of each dungeon.
Code:
Wrath of the Lich King Dungeons
Dungeon Normal Mode Heroic Mode
Ahn'kahet: The Old Kingdom - 2300
Azjol-Nerub - 1100[1]
Caverns of Time: CoS 550 1700
Drak'Tharon Keep - 2000
Frozen Halls: The Forge of Souls ? 1140
Frozen Halls: Halls of Reflection ? 1340[2]
Frozen Halls: Pit of Saron ? 1520
Gundrak - 2250
The Nexus: Nexus - 2300
The Nexus: Oculus 500 1600
Trial of the Champion 130 1180[3]
Violet Hold - 1300[4]
Ulduar: HoL 650 2150
Ulduar: HoS - 1850
Utgarde Keep - 1950
Utgarde Pinnacle 500 2000
*There are a couple of things here to note as how it is bugged on warmane.
The first column is what rep you should be able to receive, in total, from wearing a faction tabard and championing that dungeon, however some as you have mentioned are not giving rep.
The second thing about this, is from my testing, the ones that ARE giving rep, are only giving the rep if you enter the dungeon via the dungeon finder/RDF tool. And if you enter without the RDF tool, they will not give rep. This is broken/not working correctly. The dungeons that should give the rep should also give it regardless of whether entering through or not through the RDF tool.
I will make a bug report for this and the link will be below in a few minutes. The thing is to have this issue looked at, it will need to be voted up in the bug tracker. So PLEASE visit the link, vote up the bug, and provide responses there as to your own experiences with this problem.
https://www.warmane.com/bugtracker/report/34212