Symptom:
Docked window is present but in View many is unchecked

Conditions:
Erase any default config on a CUCM.

1. Create custom one. On device page in a field Cisco Support Field.
2. Be sure that DockedWindowVisible is set to falce in that config file.
3. Delete the %appdata%\Cisco\Unified Communications\Jabber and %localappdata%\Cisco\Unified Communications\Jabber directory; so you know you have a clean configuration.
4. Relaunch Jabber for Windows and login

The Show docked window is being honored, but in View menu checked box is not set. 
If you set it and un set it, everything is ok.