I just set one of these up in our office this very week, and I have no idea what you are describing in your setup...
I used the web interface to set up the phone.
I had to set up in-bound authorization in the phone system programming so that the extension number was the user account, with a password.
I also had to make sure that the cordless device was matched to the correct account within the DECT base, that's important, if you want calls to be made or received from the cordless device.
The only other weird thing I had to do was set DTMF signalling to be "in-band" in the Yealink programming, so that I could dial into auto attendants. In the 5000 programming, I set DTMF to be the RFC value.
Took about an hour of poking around before I had it operational. Next time will be much faster! And our source for this device is so much cheaper than Mitel's equivalent device.