@Bristol_Jonesey - Vlada has multiple computers, with different OS versions between them.  
 
Edited to add: I just read her signature - I think she should consider listing her other systems and OS versions.  I recall her having at least one computer that had XP on it, and then she built 2 computers with Windows 8.1 (then had nightmares and may have gone back to Windows 8 or even Windows 7).  I am not sure what she is running now.
 
Bob Bone
 

vladasyn
John, thank you for the reply. It states in the first post: "I have strong 2013 build custom computer with AMD Radeon 7850 graphic card (2Gb). It should be able to handle Sonar. I have 16 Gb of memory at 1600 Mhz, Intel 520 SSD, Intel 3770K processor (quad core). Windows 8.1. 64 bit." XP has nothing to do with it.
 
The issue started after Sonar PX3e was installed and Blue 2 by Rob Papen. My video driver Catalyst may be one version older, but nobody updates graphics every update unless they are gamers. Refresh rate was not changed. It is Sonar's behavior: some time Beat Tweaker continues playing when playback stopped (BeatTweaker is a drum program)- new issue. The running line jumps on top of plugin windows after everything blinks like software windows become inactive. Just strange stuff. Will watch it more tonight.  

I was working from what is posted in your signature. 

See if you can reproduce the "flickering" or "blinking" behaviour with no plugins and a brand new project with no template.
 
Even if the flicker issue is only Sonar and even if the behaviour just started with X3E, then I agree with John, you should be looking at updating to the latest AMD graphics card drivers and I also strongly suggest you should run Windows update several times and install the optional updates. All these could definitely be related.
 
You may even need to update your sound card drivers as well.
 
It might seem strange, but any of these things could actually be the root cause.
And if you nail it down to a specific plugin then you should also be looking for updates for that as well.
 
Thanks
 
Alex
 
p.s Yes your signature shows a different system hence the confusion.

robert_e_bone
@Bristol_Jonesey - Vlada has multiple computers, with different OS versions between them.  
 
Edited to add: I just read her signature - I think she should consider listing her other systems and OS versions.  I recall her having at least one computer that had XP on it, and then she built 2 computers with Windows 8.1 (then had nightmares and may have gone back to Windows 8 or even Windows 7).  I am not sure what she is running now.
 
Bob Bone
 

Blimey. I didn't know that Bob. I have enough trouble managing 2 systems 

SONAR is everyone's whipping boy

Bristol - she also has a GIANT bunch of midi-connected keyboards from WAY back before USB, all hooked into the matrix.
 
When she was contemplating buying some high-end computer, I talked her into building her own (two Windows 8 boxes), and she has done a remarkable job at learning and getting things done, with not all that many nightmares.
 
She probably gets a nice tan from all the glowing lights and current surrounding her.  :)
 
Bob Bone
 
 
 

And a not insignificant electricity bill