This is what I did and I just double checked this in my test environment:
Open Applescript Editor and create this script:
tell application "System Events"
delete login items
Then export that script to an application, via the export menu. I have a local test account on my Macbook Pro named, "Tom Waits." The shortname is 'tomwaits,' and I fast user switched to that user, opened up a terminal session, switched the terminal session to the root user, and opened the app from my home folder, as root, but as the currently logged in user:
bash-3.2# sudo -u tomwaits open /Users/tlarkin/Desktop/deleteLoginItems.app
In return the start up items I set for the user account Tom Waits, were in fact deleted. I had added Safari and VMware Fusion assistant as two start up items. If this is further not working for you I will toss it in my virtual JSS when I have a few minutes later today to fully test. As of right now I have only tested it locally. I did get the expected results though.
I hope this fixes it,