It's an FX chip, so don't expect miracles of speed, I don't care how many cores it has. If you application is single thread heavy that could be a reason why.
You have fixed the 10g of ram problem (seriously, when are OEMs going to stop ruining dual channel mem configs with goofy setups?) The liquid cooler and upgraded PSU are good ideas, probably not necessary for the CPU but, hey extra is almost always better when it comes to cooling.
I'd check the bios, and make sure all cores are active(some OEMs turn cores off for various, but unacceptable reasons), I would also check to make sure your new memory is running at it's advertised speed. If not, this could be a problem.
AMD chipsets(especially the low tier ones) can be finicky with mem timings above 1333/1600...you only said 16gb so I have no idea what speed or cfg used.
MB also has issues with core allocation according to some threads on their forums, version 2 seems to have fixed this for some, however, all seem to not see any CPU usage beyond Core 1...which might be bad for an AMD chip.
I wish I had better answers for you, but honestly...HP needs to stop labeling off the shelf consumer level hardware as "Workstations" just because the CPU has more than 4 cores.
Anyway, I'd suggest overclocking that FX to gain some single core prowess but I doubt you'll be able to do much with that setup. If anyone here owns one and has OC'd the unit, pipe up, he needs some help!
PS - run HDtune as well, and see if caching to a slow Hard Drive is the problem as well, if it's under 100mb/s...you might want an SSD for the OS and use the HD for storage.