Having the same problem since Cubase 8. I am on Cubase 9.5.1 now. Happens randomly.
If the problem occurs for a specific track in a project one time it stays.
Big Problem. Even creating a new track and copy the track settings do not help.
Wondering if there aren’t more people having this problem. I gave up hope that Steinberg will solve this,
but at the moment I am stuck with a Mix for a client and having this problem on 4 tracks. I can not go on working.
This problem occurs with all combination of plugins. There seems not to be a specific reason. Even the latency is much more than the plugins on the track would add. The tracks are just completely out of sync for more than one bar.
I guess this problem only occurs if you have a Bus where all tracks some kind get routed too. A Mix Bus where all tracks get summed.
Then this one Bus is sent to the Stereo Out of Cubase. I always work this way for years and since I do so this problem occurs randomly.