All that having <99% gpu usage means is that at one location in the overall pipeline of your GPU (the point where the measurement is taken ... wish I knew what that was, but I don't), that particular component is not running at full capacity.
Therefore, SOMEWHERE else in your PC, or even elsewhere within the card itself (for example, if you were memory capacity or bandwidth constrained), you have some kind of bottleneck going on.
Something that's important to remember is that GPU usage isn't really a measurement of the usage of your entire card, all at one time. A video card is like a miniature computer within your computer, with tons of subsystems that could act as bottlenecks and you'd not know it was happening because you're not taking usage measurements at all these subsystems, you're just measuring at one point that is 'expected' to be most representative of usage of the total card. But it's a 'guess' because different subsystems get stressed differently by different games/tests.
Driver and game code can also play a big role in how well your 'card' is being utilized in any particular game. Playing over the internet can also add potential for an additional source of BN.
So, while CPU BN is a logical 'first place' to check when your GPU usage isn't at 99%, because it's the most common source, it's FAR from the only possible source. And sometimes even a CPU BN can actually just be caused by buggy or unoptimized game code (see Skyrim for a great example ... it used to be HUGELY CPU BN'd at certain places, now it's patched, and that issue is fixed).
As long as things like Heaven and 3dMark11 tap your GPU out at 99%, then your system is almost certainly working fine. If you want to spend countless hours trying to figure out why you only get 80-90% GPU usage in Crysis 2, knock yourself out.
Here's your simple testing options:
1) bumping your overall CPU speed upwards through OC'ing,
2) switching drivers or patching the game
3) trying different game settings
to see if any have an effect of increasing GPU usage. If none of those work/help, my advice to you is to let it go. Because you can waste HOURS of your life trying to run this 'issue' down, and never find a 'solution' because it cannot be fixed by people with the expertise of you or I
Also lower than 100% CPU Usage in Task Manager does NOT mean you DON'T have a CPU BN going on, so don't fall into the trap of thinking that.