So, I got a new computer (from ADK) with TB and an Apollo DUO. The system screams but I was having intermittent drop outs in a complex mix (with many VSTi's and UAD plugins).
I tried everything I could think of... raised the latency (which didn't fix it but reduced the number of dropouts). Updated all my software to the latest versions. Updated all the drivers on my new PC to the latest drivers. NADA...
Then, I stumbled across the mix thread count variable in the AUD.INI file. Read a blurb from Noel. And set this to use only 6 threads instead of all 8. Thus reserving 2 threads for the OS and other tasks.
And VIOLA, FIXED... I even turned the latency down to sub human values and the system now screams.
So, before you give up on SONAR and dropouts. Try using this variable to reserve some CPU power to overhead.
Hope this helps some other frustrated SONAR user.
Jim