I have roughly the same graph.
It is obviously a windows problem. This is my scenario:
I bought two 840 120GB's. Put them in raid0, 16k slices. Everything went sweet and got speeds up to 1000MBps.
But I knew it wouldnt matter much with a single ssd. Figured I buy a 250G one, clone the raid array to it, I'd be good. Of course I'd had to set ahci back on. And I'd put one 120G ssd in my laptop, and sell the other.
Now after cloning I noticed fan speed fluctuations. CPU was getting hot, turbo got switched on and off. Investigation pointed to windows not being set to deal with ahci properly, and the intel drivers/matrix storage software prolly just eating up resources. So I removed intel matrix storage and rebooted. Still no change. After some more minor tinkering and trying (dont think any helped) and another reboot (yep that must have been it), things are looking up and cpu is running smooth again.
But still, that wonky graph from hdtune. It is still not good. I had ssd's before and hdtuned them, it's not right to have such violent spikes.
Since the only thing really different is how windows gets along with the drive in a nice anhi way versus the raid array, I should be able to find it and fix it. The sure fix would be to reinstall windows. But for me that's a last resort.
So I suppose I'd be looking for driver issues, windows settings for raid that need to be reverted, check put the ssd, optimise it and what else can I try?
I hope TS might recognize something here, and get new ideas to fix his problem.