Did you try, if a complete clean new advanced setup does work?
discuss.answer
UPDATE:
I decided to spin up another server and install on that. It all went perfectly.
Really bizarre as we use ansible for provisioning each machine, meaning the setup/software was exactly the same.
I'll be keeping an eye on that particular project/server now (I don't like not knowing what actually caused the problem).
Again, thank you all for your help. I think I'm gonna hang around here more.
Matt
I wonder if one of your plugins might be causing the problem. I think some parts of Setup cause System Events to fire. A plugin connected to one of those events will execute, but MODX isn't really in a normal state (for example, there may be no $modx->user or $modx->resource), so the plugin executing at that point may crash.
I've seen this happen more than once with upgrades, though it's not very common.