I'm having the exact same issue. The paths in Vista are all different. I've created a config.ini and preferences.ini and put them in:
C:\Program Files\VMware\VMware Workstation
With the line:
mks.noBeep = "TRUE"
This is driving me insane!
beep beep beep
I even tried to disable it in the bios, and removed the alert in windows, and I disabled the beep device in the device manager. Nothing works!
I'm running Vmware workstation 6.02 and running Vista Home Premium...
YES YES I FOUND IT!!!!!
Add mks.noBeep = true
IT'S GONE!!! GOOOOOONNNNNNNEEEEEEEE!!!!!!!!!!!!
laughs and cries in the corner
What you can also do is on the VM machine just type net stop beep and your beep is someting of the past!!!!!
I was having the issue of my VM beeping despite mks.noBeep = "TRUE" already being in my preferences.ini file
Your solution of 'net stop beep' worked for me in Windows XP also.
system beep is the worst feature imagineable, than you very much for your help.