Hi,
Having a similar experience with an Apollo 8 Thunderbolt; being a sonar user for years and got dropouts every start/stop. Unable go lower than 512 buffer size if *i want to be able to work with normal decent projects (20 tracks with virtual instruments and audio, processed through existing plugins, nothing too fancy). Even if the DPC latency reports very good measures (lower than 100) I still got dropouts... I tried with Studio One and got some weird results that I did not explain either until I decided to go deeper and rearrange the graphic card on another PCIe port and my SSD drives through the same interface. Now everything is super smooth on Studio One up to a buffer size of 32 but I still have the same results with Sonar. I will try to stress up the setup with Studio One to see how it behaves on heavier situation but I do think something is wrong with the way Sonar deals with TB interfaces.
I will also try to give a shot on how Reaper behaves on my system too...
Best,
Stéphane
MB used: Gigabyte Designare EX X99