The execution path could be different where the file is located.
In your case, the execution is in /System/.../MacOS/Python
however your file is somewhere else. This misbehavior could be resolved if you use the full path of the file.
Let me assume, that your file is located in your Desktop. Then this is the modified code that uses absolute path.
import os
def hmsbookings() :
os.system('python os.path.expanduser("~/Desktop/hmsbookings.py")')
root.after(60000, hmsbookings)
I'm not familiar with macOS, I based on this question. If you need more information about absolute path on mac see this question.