Did you use any 3rd party plugins in your project?
also check your drive activity - maybe the HDD's are too slow to keep up? second one would be a plugin...
keep in mind that there has to be something for your CPU's to do...
for example if you have changed to MPE GPU accelerated your CPU's no longer have to scale your video to output resolution - so no 100% CPU usage - but maybe some on the GPU...
There are zero plugins (other than audio dynamics I always use) and zero scaling. It is straight AVCHD 1080p footage synced with externally recorded audio. Nothing has changed in my workflow, only the fact that CPU usage during my normal exporting was nearly 100% and now it's averaging about 35%. At 100%, exporting was nearly real-time. Not anymore.
I don't really have an answer for you, but for comparison purposes I'm running a pretty similar scenario with CS6, AVCHD files, a Z800 with two 2.4ghz processors and only 12gb of ram. I'm exporting an H.264 1080p file right now at a relatively low bit rate of 1.5mbs and it's using around 95% of my CPU. I do find that I have better luck and speed with exporting from within Premiere vs. Queing to the standalone media encoder. I don't know why that is and I haven't experimented as much with the new encoder. I was using CS5 and found the encoder would sometimes crash on a video export but I could export fine from within Premiere. I haven't done a real scientific side by side comparison but my sense is the program Export vs. Que is faster. Anyone else have that experience?
I'm doing a similar export right now as I write this. It's a two camera shoot, and one of the cameras was a little noisy. For that reason I'm processing images from that camera through NeatVideo.
When the footage is coming from my Acam (the two shot) AME ramps up to nearly 100% CPU and just hauls ***. When the footage is coming from my Bcam (the one using NeatVideo) AME can only manage about 50% CPU. I can watch it ramp up and down in Resource Monitor.
I'm doing this work on a i7-930, Win7, 12GB RAM, three disk drives. The CPU usage is aroung 50% (eight hyper-threads, all more or less the same). I'm showing more than 2.0 GB of RAM free, and the disk drives are all averaging very close to zero active time with queues that spend more time at zero than they do active. In other words, I'm not blocked on disk, memory, or CPU. But I am evidently blocked on software. That would be NeatVideo. I suspect that some of what it's doing to each frame can not be parallelized. This would, to some extent, serialize the frame flow, which might (I'll say that again -- might) account for the slow down in CPU utilization. IDK.
But when the footage has just the luma curve and three way color corrector effects running against it, PPro / AME just hauls ***. I've measured around 10 frames / second.
Another way to slow down an export from PPro is to use AE via dynamic linking. It seems that when you do this that the AE that gets called up to do the processing for the export runs on just one hyperthread. There are other discussion threads about this; you can find them if you search. I bring it up only because it has somewhat similar symptoms to what you are describing.
So... I don't have an answer for ya. But I feel your pain.