Basically just what I said in the title. I have an absurdly simple example of this happening for me:
print("test 1")
plt.pause(2)
print("test 2")
fig, ax = plt.subplots()
print("test 1")
plt.pause(2)
print("test 2")
When I run this, it pauses for the first test print, but does not pause afterwards. This showed up in a more complicated setup, but it happens even in this sort of super simple situation.
Edit: to be clear I need plt.pause to work because I need to be able to get figures to update; I'm not just trying to pause execution. My code here doesn't show any plot updating because the issue isn't in that part of the code (debugging and manually pausing execution causes plots to update normally) and I wanted to find the simplest case where pause doesn't work. Sorry if that was unclear.