I had to re-read this 3 times to make sure I understood what you were saying... You mean you can't control the deskphone (answer, place calls, etc) from the Lync plug-in? I have never had to do anything special to make this work, just install it, login, and it works.
If you look in %appdata%/Mitel/UC/uca.log does it show anything weird or any error message?