It sure sounds like something is sucking up resources when you're accessing the EQ controls.  Does this happen with both the regular and flyout in X3?
 
I'm not sure if this something you are able to try this, but perhaps a cheap dedicated graphics card would be worth a shot. 
 

So are you running X3D now?

Hi Daylaa,
My gut feeling on this is that it is an installation issue. It's possible that the EQ has installed on a particular part of your HHD that may be difficult to access when Sonar is calling it to RAM. Just a thought, it's not an unheard of fault. Have you ever had to do a reinstall or is this the original installation of Sonar and/or Windows?

Really reaching here, but is it possible X3 is somehow accessing the wrong version of the EQ?  Not sure if there were any changes between X3A and X3D to the eq, but I have discovered a few oddities when I tried to open a file made in 8.53.  The EQ verrsion was older even though I thought I had purged my computer of older versions.

+1 Dub.... and I think this is the file????
C:\Program Files\Cakewalk\Shared Utilities\Internal\PCS-GlossEQM.dll... I'm on version 1.2.2.278
 
The obvious thing here with "D" is 64 bit precision engine (apologises because the first rule of 64 bit precision engine is you do not talk about 64 bit precision engine).