Hi Jesse,
Sorry for the delay, but here are some suggestions to try - first, like you already did, you can increase the maximum threads on the supervisor even more, perhaps to 128. Just note that the more threads, the more communication can be handled, but the more resource-intensive the supervisor service becomes.
Additionally, if you are able to remove any old jobs, that should increase performance. Finally, we have made a number of performance-enhancing changes to our Qube 5.3 version supervisor, so if you have not yet upgraded from 5.2, you might consider that.
Hope this helps!
-Jason
PipelineFX