Audio problems up to my ears....

Hi All,
 
You guys are always very helpful; so I'm hoping that this tyime is no different (...no pressure:))
 
Here's a quick lowdown...
 
I'm running sonar 7 PE, on an HP slimline (3.06 GHZ), focusrite sapphire 6 as an audio interface.  Plug ins are: EZDrummer & Peavey Revalver MK III.V.  If this helps; audio settings are: Sampling rate: 44100, buffers in p/b queue: 2, buffer size: 12.1 msec.
 
My computer crashed a couple weeks ago. It wasn't related to sonar, it wasn't open at the time & I hadn't even been using it that day.  When I took it to the repair shop, they backed up all my audio and cakewalk files.  After doing a factory restore and installing all the programs and files again; I set about trying to get back to work.  I found that all the audio seemed to have popping and crackling on it, that was definitely not there before.  I screwed around a bit (shutting down and powering back up, etc.)...no dice.  So, I tried mixing down one of the tracks to a .wav file; just to see.  Strangely; no clicks.  It sounded perfect. 
 
Here's the problem.  The playback still had all the noises, which made tracking extremely difficult.  The cursor bar would also be way behind the audio I was hearing.  When I tried to record a track, the sound clip was not only starting later; but even when I would line it back up, it was out of time.  I would have to slice up the clip & keep dragging the slices to the left to get things sounding in time.  I know guitar players aren't supposed to be able to keep a steady tempo; but this also happened with a synth using an arpeggiator that was set to my DAW's metronome tempo.   
 
After reading a few posts that claimed similar problems, I tried runnig the dpclat latency tester and it said my computer should run audio fine without dropouts, etc.  I then tried to change the driver from WDM/KS to ASIO.  This seemed to work, at first.  There was no noise, although playback speed was a little wonky.  However, when I tried to mix down and play it back, there was no sound.  It looked as though a track was playing in windows media player, but no sound.  So, I changed back to WDM/KS and now I get no playback sound at all....anyone got a shovel, so I can dig this hole a little deeper?
 
Any suggestions are greatly appreciated.
 
~Iain

As Dave has said, obviously the OS restore has undone your prior settings and configuration that had Sonar running smoothly. 
There is lots of info on optimizing a PC for audio. Dave has supplied a few great suggestions so start with those for sure.  
The stupidest things can screw you up. You can always turn stuff back on later. Google "optimizing PC for Audio" for more info.  
The first thing I always recommend is running the DPCLAT test which will usually route out issues with background processes interfering. But sometimes it does not detect everything ( so I've been told) Try running it with Sonar open and the Sapphire powered up.  

I am assuming you are using XP 32 bit ? correct? 
Always start with making sure your ASIO drivers for the Sapphire are up to date and the correct version is installed. This is very important!  It is best to stay with those ASIO drivers. 
Disable your on board card for now in the Device Manager. 

Open Sonar and make sure the settings are correct for using the Sapphire and ASIO. 
Check share drivers with other programs. 
Go to the Sapphires control panel  via Sonar ASIO button. 
With your older computer you'll want to use "safe" settings. ( 44.1/24 and medium latency)  

Oh and always use the same USB port that you first used to install the drivers, Make sure it isn't being shared with a bunch of other stuff. 
Not all ports are created equal ( so I've been told)