Yep, this is a major issue. I ran into it when trying to get blue drakes for my teams by getting Occulus from the Random Heroics in the months before Cata came out.

I started keeping a log of which "randoms" I got each time to track exactly how bad it got. I was able to do this on four teams, so it didn't take THAT long to queue over 200 times, but still, it did take a while.

Random Queues: 204
Occulus Hits: 4

Given the number of heroics out there, with 204 queues I should have hit each 13 times on average if they were equally weighted. Obviously, they weren't. (I'm looking at you, Old Kingdom, which came up more than six times as many times as Occulus).

I can kinda see why they do this, but it turns out to be:
Blizzard: Ah, I see you really like some of the heroics I created for you. Well, to the extent you enjoy them, we'll do our best to ensure you rarely get them from the random heroic. The ones you hate the very most? Ah, we'll make sure you get those a lot! After all, we designed this game for your enjoyment.

It is for this very reason that I'm not entering any dungeeons as I level up with my 2nd team (currently level 84.5). My strategy will be to try to get one of them at least the minimum gear to queue for random heroics without entering any dungeons. Then I'll visit the entrance for only BRC and Vortex Pinnacle, sub him in for one of my heroic running team members, and queue up. Since the number of heroics available to that toon is very small, my hope is to get the heroics I want. Then I can sub back in my 5th original group's team member (though that one team member won't get the random heroic reward). As I figure out other heroics, I can visit those entrances with my new level 85 heroic queue guy.

Trying to be creative in beating the system until I figure out other heroics.