Ok, interesting to hear that it is working fine now.
We've had issues with GUI sluggishness and freezes on El Capitan in the past, which we have done our best to work around. The problem is, in any DAW the audio rendering process is always guaranteed to be run, but the process controlling GUI updates is given a much lower priority. El Capitan introduced tighter constraints (at an OS level) to the process running the updates, so if your CPU is very busy, the OS will start dropping GUI updates. As I've said, we've done a number of things to mitigate this, but there's no real "fix". My guess is that previously your CPU was under a heavier load (either form a large session, or other applications running simultaneously), and most recently it wasn't. Let us know if the issue persists.
Also as a warning, I would recommend using the VST version of Blackhole in Live. There's an annoying bug in Live where when duplicating clips on a track with Blackhole AU, the Input/Output sliders will snap to -60. We've talked to Ableton about this as the issue seems to be coming from their side, but the easy workaround is to use VST – it doesn't have the problem.