I dont think you can stop this, but you could login in on each computer as an administrator and configure the phone manager software. Export the registery setting for the phone manager and save as the extention number. Then in the login script use the %computername% to install the relevant registery entery if using windows nt or in the computers startup group instead, this way when they logon to a computer the phone manager will be configured to the phone that is next to the computer. I would also set the working directory for the phone manager to there home drive so that there personal phone directory's still move with them.
You could also just logon the phone as there normal extention.
I hope this helps