Probably not related to the Organizer tool. The purpose of
Organizer is to allow you to copy styles, macros, autotext,
toolbars, etc., from one template to another, and you're not
doing this.
After you change the default font, are you prompted to save
changes to your Normal.dot global template, and do you say yes to
the prompt?
Is Adobe Acrobat 7.0 installed on the computer? If so, the
Acrobat 7.0 Create Adobe PDF toolbar add-in for Word prevents
Word from automatically saving changes to the normal.dot template
.. Choose your preferred font again, set it as the default, and
click "Shift+File | Save All" to force Word to save the
normal.dot template. Alternatively, you can prevent the Adobe
add-in from loading by editing the Windows registry key
"HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Office\Word\Addins\PDFMaker.OfficeAddin"
and changing the "LoadBehavior" subkey value from 3 to 0, but
you'll lose the PDF toolbar if you do this.