Can I clarify one point?
 
You say "Sonar does not have to be running, I get pop ups from Win Patrol every couple of minutes that it is trying to change."
 
How then can SONAR be requesting a change if it's not running?

I'm not allowing the association to change.  Win Patrol pops up with the notice and I deny the change.  But a couple minutes later Sonar tries again and I get the pop up again.
 
Its not a false alarm. 
 
I'll wait and see what response I get from Cakewalk on my open report   CWBRN-32777.  I just opened it late last evening so it may be a day or so before I get a response.
 
 

The report is that "Sonar Platinum" (SONARPLT.EXE %1) is trying to associate itself with the .mid file type.

Try turning off automatic VST scanning. Just a hunch as you say it's trying to do it every few minutes.
I would also give your system a FULL scan with a virus scanner AND Malwarebytes (check root kits as well in the settings), and you may also have another utility running which is conflicting...
 
http://billpstudios.blogspot.co.uk/2007/09/don-change-my-file-type-associations.html
 
I'd also try allowing it to see what happens. It might make the change and then it might get changed back.
 
It could be a Sonar issue, but have to admit being rather sceptical about Win Patrol though ...
 

If Sonar is not running then I'm not understanding how it can request an association change.  I would think that if Sonar's exe file is making the request that it would have to be running to do that.
 
I have never seen sonar's executable file run in my task manager unless I physically have opened it myself (or in the case of older versions where it wouldn't shut down if you still had a MIDI channel open, but that's a special case different from what the OP is describing).
 
fireberd - I'm not trying to say you're wrong, but I would suggest that you search alternate means for the reason this is happening.  and it seems to be happening only to you since no one else can confirm it's happening to them. 

Well, I fixed it.  I rolled back to the previous version and then rebooted the PC.  No .mid request from Sonar.  I then reinstalled the Dorchester update.  NO .mid requests.   However, I had to do this on both Win 7 and Win 8.1.
 
 

@Beagle - Yes fireberd is not being clear here whether it's happening when Sonar is running or not. He says "Sonar does not have to be running" and yet he says SONARPLT.EXE %1 is trying to associate itself with the MIDI file. I hope he checks #14 regardless.

fireberd
Well, I fixed it.  I rolled back to the previous version and then rebooted the PC.  No .mid request from Sonar.  I then reinstalled the Dorchester update.  NO .mid requests.   However, I had to do this on both Win 7 and Win 8.1.

Seems a bit extreme, did you not try #14? Did you try letting it happen (you could have always changed it back). Regardless glad it's working for you.

Well it appears he did do it:
http://forum.cakewalk.com/FindPost/3214454
 
It's really annoying having two threads about the same thing, it just splits the communication.

I posted one of these in the Sonar forum section.   The other one was posted in the problem section.  The moderator must have moved it to the Sonar forum section and the reason both appear.   I didn't post two of the same in the Sonar Section.