Daylaa
Just went back into my power management settings again and this time it said '100%' so I may have accidentally been looking at the 'power save option' (5%) before. It says I have 'High performance' active.

Change your minimum processor state to 100% and the dropouts should go away. 
 

Paul P

Silicon Audio
Disable variable speed settings like Intel Speed Step and AMD Cool N Quiet in the BIOS setup for more accurate results.

 
What affect might this have on fan noise ? 
 
 

Don't worry they will still be queueing for autographs.

Paul P
What affect might this have on fan noise ?  If you set your CPU to run full blast all the time, won't it run hot ?

Paul, for me, I can set the System and CPU fan speeds at different temperatures. When I'm tracking, I don't use FX inside Sonar. I use the Reverb in my Interface. I sometimes output soft-synths or metronome clicks from Sonar. I turn off everything in my PC I don't need and reduce the fan speeds at lower temperatures. I leave the fan speeds where they are at higher temperatures, but my PC doesn't normally reach them when I'm just recording a band.
 
When I mix, I run with everything on my PC Enabled (like Gobbler) and the Fans at their default levels.
 
To tell the truth, the loudest thing I have is the heat pump in my house. When I know I'm having people over, I crank the heat until they arrive and then turn it off. It gets steadily cooler, but it's quiet.

Off Topic:

Location: Derby, UK (Pronounced 'Dah-beh') 
If it's pronounced "Dah-beh' - then why isn't it spelled Dah-beh?
 
Perhaps it should be pronounced Der-by.
 
 
Just sayin'...

Jimusic - I will let you off on this occasion simply because you are from Vancouver (or thereabouts) and I used to live there too. And it's great.
 
I have already looked at the minimum processor speed and mine is set at 100%.
 
Can anyone comment on why my Windows Media Player pops? Does this indicate a possible soundcard issue?
 
 

If you were handy with PC's and reinstalling the OS and everything, I would suggest that because of the amount time you've spent on this.
 
Obviously, by spec, your machine is just fine. But something is just wrong. If you try/or have tried the separate interface and it still doesn't work (I think you did an X3 re-install as well), you may want to considering bribing an IT friend to redo your machine. I am in IT and at a point, the time trying to solve a problem(that doesn't seems to be one the majority do not have) is not worth it and a "nuke and pave" is in order. 
 
I am aware that involves a lot of programs to reinstall and such, but may be a better use of your time. Sometimes these bloody boxes have GREMLINS in them.

hockeyjx
If you were handy with PC's and reinstalling the OS and everything, I would suggest that because of the amount time you've spent on this.
 
Obviously, by spec, your machine is just fine. But something is just wrong. If you try/or have tried the separate interface and it still doesn't work (I think you did an X3 re-install as well), you may want to considering bribing an IT friend to redo your machine. I am in IT and at a point, the time trying to solve a problem(that doesn't seems to be one the majority do not have) is not worth it and a "nuke and pave" is in order. 
 
I am aware that involves a lot of programs to reinstall and such, but may be a better use of your time. Sometimes these bloody boxes have GREMLINS in them.

Hey Hockeyjx.
 
I WISH I knew more about PC's. It definitely seems like the folks on here who have the 'know how' definitely have a better experience of Sonar. I never imagined upgrading my home studio would be such a technical nightmare. 
 
Just to update you - I am using X2, not X3. And I am yet to do a full re-install of X2 because I'm not confident enough to do it (unless you could kindly show me/tell me how.) I would like to do this.
 
The guys who built my PC (Rain) remotely accessed my machine a couple of weeks ago and said they could find nothing wrong. However, why is a machine as powerful as mine experiencing such annoying issues? Popping when starting/stopping audio in Windows Media Player is the latest?!
 
I am also yet to try a different audio interface because I can't get hold of one to borrow. I even went into a music shop and asked to 'rent' one. The guy gave me a strange look.
 
 
 

Makes me laugh that you asked to rent one. On the other hand, bring in a mic a mic cable and your computer and hook it up there (?) if it's possible. I did that when shopping for interfaces for my laptop. People were very friendly about it. I do it when shopping for mics too. I go ahead and record a sample right there in the shop and then take it home and compare on my stereo to see how it sounds to me before I buy.

Daylaa
Jimusic - I will let you off on this occasion simply because you are from Vancouver (or thereabouts) and I used to live there too. And it's great.

 
I was hoping you'd get a kick out of that!  Can't imagine you'd leaver Vancouver or surrounding areas or anywhere in BC, unless you had little choice in the matter. 
 
But sometimes you gotta do what you gotta do.
 

Daylaa
I have already looked at the minimum processor speed and mine is set at 100%.
 
Can anyone comment on why my Windows Media Player pops? Does this indicate a possible soundcard issue?
 

 
 I'm sorry - I wish I could help.
 
I too think I had the same thing happen, but never found out what it was.
 
My sound card is in top notch shape though, so I don't think that's it.

Hey folks - I have just installed X3 Producer. I've not yet installed any of the updates.
The Pro Channel is behaving VERY smoothly! I'm actually thinking it may be fixed!
I may be speaking too soon, but this is pretty huge for me.
8 months of technical hell may have come to an end!
It's quite possible that my issues were caused by X2 alone.
Here's to hoping my musical career can start again!
Will keep you posted.