I have the same case and had a similar issue - as far as I could see, the case's buttons were aligned correctly, but the lock button in particular had no sense of movement or feedback, so it required a very hard press to actuate it, and the only way of knowing that this had been successful was to look at the screen.
I contacted Otterbox via their website, explaining my problem. They responded very quickly and sent me a replacement case. The new one is very significantly better and now the lock button feels more tactile and positive. It's still far less clicky than the phone's button without the case, but I think this has to be expected and I'm now perfectly happy with it.
Whether they've had a bad production batch, or whether they've recently improved the design, I don't know, but I suggest you contact them.