Lock Manager uses lock-user.groovy since it (lock-user.groovy) is a child app.
Hmmm ... never had that problem. You might pose that question to Erik in the Lock Manager [beta] thread. The only thing I can think of is to reinstall everything and make sure you change the device handler to "Z-Wave Lock Reporting" for your Yale lock(s) in the IDE.
BTW, which Yale lock model do you have?