Hi,
this might be useful for the one or other person as it bothered me several days now (I have SP3 and the proofing tools installed, also I've never noticed that issue in the past).
If you install Office 2007 in a fresh bottle (CX 12.1.2), all the file association (docx etc) are correctly set and files can be opened via file manager ala Nautilus.
However, after the installation of Visio 2007 into the same bottle, most of the associations stop working and also disappear from the Crossover Control Panel -> Edit Associations menu.
I assume that the "correct" solution would be the separation in two bottle. For me it helped to install Office 2007 again and to select the "Repair" menu which is available when it's already installed. After that the file associations are working again.
Best regards.