I hadn't yet checked this, but it seems regular hyperlinks in Word do launch Mozilla Firefox. So in Word, it's only the e-mailaddresses that keep open up in Google Chrome.
Maybe your situation could help me. Do you have FF set as the default browser? What browser is launched when you click an e-mail link within Word?
What programs appear in the window to change the program associated with the MAILTO protocol? Do you have a 'Browse...' button there?