If chkdsk is stalling it's not a good sign and Sonar isn't going to be related to this, it could be chipset drivers in retrospect (I assume the USB drivers didn't come with their own drivers, if they did check for updates):
... and please run this:
http://forum.cakewalk.com/Driver-Boost-m2928792.aspx
 
If it updates your chipset drivers etc please run chkdsk again after you've rebooted a couple of times....
Also your hard drives may have firmware upgrades available on seagates website, get the make and model numbers out.

I installed and ran driver boost the first day I saw it posted here!  Awesome program!!!

I not sure but I thought one is not to use Chkdsk on SSD drives.  

John
I not sure but I thought one is not to use Chkdsk on SSD drives.  

SSD's do not get defragged, and by default, Win 7 excludes them from automatic defragging. My intel drives have software that is used to manage their health.

John
I not sure but I thought one is not to use Chkdsk on SSD drives.  

Yup I think you have a point....!!
 
http://www.tomshardware.co.uk/forum/284051-32-chkdsk-usage-intel
 
So you've done driverboost...
Check seagates site for firmware updates I suggest then.