Testing 4x E5-4650s and 128GB RAM - tweaks for 32-core performance?

Howdy. I've got the following system:
4x E5-4650 eight core CPUs (32 cores/64 HTs total)
16x 8GB EEC RAM - 4 sticks per CPU
2x 512GB Samsung 840 Pro SSDs
5x 3TB Hitachi HDDs in RAID5
1x GTX 670 w/ 4GB RAM
Windows Server 2012
When I'm exporting 1080p from Premiere Pro CC with software encoding I'm getting really low CPU usage - around 4% usage, If I enable Mercury Engine it jumps to about 20%. Any tips or tricks?
*EDIT: I'm exporting from various sources and frame rates to 1080p H.264@50fps I'm happy to run some tests.

Just finished PPBM7 and got the following:
Disk I/O Time = 244s
Premiere disk write rate is 152.02MB/s
H.264 Encoding = 126s
MPE gain = 293/97 = 3
The disk I/O time is strange as I get the following with CrystalDiskMark:
While doing the PPBM disk test this is the disk activity reported:
It seems to average out at about 500MB/s according to the resource monitor but only is shown as 152MB/s? It also has the OS on it so that might be an issue. Here are the ATTO Benchmarks, which seem pretty on the mark for the specs:
I think there are definitely major changes needed to get better performance out of this system. I'm just running a few tests now and it seems that Windows 2012 is pretty shocking compared to WinSvr 2008: Supermicro X9QR7-TF+/X9QRi-F+ vs Supermicro X9QR7-TF+/X9QRi-F+ - Geekbench Browser
Having a look at the benchmarks for the 11TB RAID5 shows some amazingly bad performance - 11MB sequential write, 200KB/s random 4K write. I get better write speeds on my USB stick. Either CrystalDiskMark is screwy or the raid setup is totally broken. It's setup using the onboard LSI 2208 controller, which I though was pretty decent. I'm guessing since my disk is 92% full that really messes with performance:
ATTO gives clearer picture, with transfer sizes below 32KB being crippled to under 1MB/s:
But of course when I copy a single 40GB file from the RAID0 SSDs to the RAID5 HDDs I get this, which I'm totally ok with:
Anyway, the major issues is really that the CPU is really underutilised and only uses about 30%. It's over 80% on one of the NUMA Cores but only 25% on the others. Looks like this:
I suspect that Premiere Pro is only detecting 32 of the threads, not 64. In the Multiprocessing preferences in After Effects it only shows up as have 32 logical processors, not 64. Thinking I'm having the same issues as this guy (same mobo and processor): AnandTech | Trials of an Intel Quad Processor System: 4x E5-4650L from SuperMicro
Any help would be appreciated.

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