Trace of random program always stays open & prevents shutdown

[classic_henry]

The only way I can shut down my machine (iMac, 10.10.5) is with sudo shutdown -h now. Some program will remain open after > Shut Down.... It's never the same program and there's no apparent pattern behind which program remains open. One day it's iTunes, the next it's Preview, etc.

Steps I've taken to diagnose/solve the problem so far:

• Force quit won't work (only an option from the Force Quit Applications window since the Dock doesn't recognize the app as running),
• cmdQuit from HamacaSoft doesn't recognize the app is running,
• kill -9 in Terminal doesn't recognize that the process is running
• killall -KILL Dock won't free up the app for force quit either

Is there some process I'm missing? I've ran a Malwarebytes scan and it doesn't detect any files or infections that might explain the issue.