I have been using Onyx ever since my first mac in 2007 so I'm very well versed with what it does and how it works.
I recently updated to El Capitan and have run Onyx at least 2x since then, and yes, I updated my Onyx immediately as the first step.
I just went to run it again and it hung up on the 1st step, verifying disk - and again, and again, and again. each time I had to Force Quit until even that didn't work any more - I had to power off several times as this kept repeating itself.
I removed the Onyx from my app folder and downloaded it all over again. When I started it up, it immediately showed the progress bar 1/3 of the way thru, where it was before, and hung up, same as before, and again, I had to power off and restart.
This time I went to Disk Utility to verify my hard drive just in case something was wrong there - it came thru fine - which it should, it's less than a year old.
What gives? my Onyx seems to be broken - is there something else I can remove to make sure it's completely off my system before re-installing?
You say you "updated" Onyx. Since you say you've installed El Capitan and not Sierra, you should be using the Onyx version for El Cap, which is v. 3.1.9 (the updated version for Sierra is v 3.2.5. If you're on the proper version, go to ~/Library/Preferences/com.titanium.OnyX.plist. Delete that prefs file and try relaunching Onyx again.