Do you see a green Z anywhere in your mixer? Are you using software monitoring for virtual instruments (which would make them green Z monitored?) If so, you could be running into the latency limits of Green Z monitoring. Plugins will start to be disabled in the monitoring path if your latency rises to a certain amount.
For songs where I need to run VSTis through mix bus processing, I set them up specifically so this will all operate within the constraints of Green Z monitoring (because I find it more useful than turning off Green Z/Dropout Protection by setting it to Minimum)
If none of the above works or applies to your situation, hey I tried!