I think restricting the backgrounds to PHB2-style backgrounds is a poor idea.
I totally buy the argument that some of these backgrounds are possible to use cheesily, so perhaps you'll want to ban or modify a few.
However, the PHB2 backgrounds are singularly worse: they're terribly boring. Look, if you just want people to get an extra class skill or two, just say so. Prepackaging them like that just makes for bland characters; what happens is that people actually look through these published backgrounds and take those that exist rather than whatever they've come up with. The character builder exacerbates that flaw.
Many of the published backgrounds make no sense whatsoever, particularly those that follow the PHB2 guidelines. Regionally associated skill just don't work - they kind of suggest that every adventurer from that region must somehow be good at these skills - as if the region is full of detectives, cutthroats, athletes, acrobats, or whatever. In any case, I'd much rather the players read various backgrounds purely for fluff inspiration (incidentally, that was 3.5's PHB2 approach) and let them come up with a an appropriate bonus - or even just choose anything - after all, the bonuses are mechanically limited so you don't need to find any preexisting background.
I find the "associated skill" mechanic distracts from the actual background.
The backgrounds of the scales of war and the forgotten realms may include one or two "too obviously good" choices, but apart from that, they're at least distinctive. I'd much rather have that than a "boring and undermines fluff" background.
And almost all of them are going to be pretty reasonable. Sure, maybe some of them grant +1 to init or +1 to two skills and both of em become class skills. That's... not exactly a balance problem, IMNSHO.
Even the so-called "problematic" backgrounds aren't really. If somebody likes making nifty super-powerful combos, these backgrounds are unlikely to stop them, and unlikely to raise the power to the next level. Windrise Ports may seem like ZOMG game changer, but that perception is skewed by the fact that any power gamer can see that it enables new combinations, which is just asking for looking for the best stuff - so naturally, you'll see some powerful combo's on boards. But even without it, there'll be a bunch of other combos to execute: I very seriously doubt that banning windrise ports (for instance) is going to actually improve any groups game.
So, I feel the various different ability score as HP score backgrounds are a little too impactful at low level, but other than that, I really don't see an issue - and I'm strongly opposed to the PHB2-outlined boringness and inappropriate bonuses that most backgrounds grant (which people will still skim for the skills they want anyhow).