Hi,
I had similar problem 2 weeks ago and as I also have a mac, I can share my experience... I have one dedicated partition for windows (using boot camp), but I can also start it in emulation (I am using VMware). It effectively seems that the search of the link station performed by the firmware updater is NOT WORKING when running windows through VMWare. It never finds the station. The problem is the same when using Buffalo NAS navigator in emulation: no disc is found.
If I start natively on the same partition (therefore, everything should be the same, except the absence of the emulation layer), it finds the station correctly.
Even when this is working, I needed to pay attention to 2 things:
1) During the first attempt to flash the firmware, it seems that the station changed its IP address in the last step and therefore the final procedure failed (however, I think that everything was flashed before this final procedure).
2) In case of such failure, If you want to reperform the upgrade, you need to change the "lsupdater.ini" file, setting teh "VersionCheck" parameter to 0 instead of 1...
3) Finally, after firmware reflash, the interface was in japanese... you have to set in in English. There is a description how to do that in this forum in the FAQ if I am not wrong.
I think it is really time for Buffalo to release a OS X version of the firmware updater... As a firmware updater doesn't require much UI, if the language used to code the firmware updater on PC is portable, this should be very difficult to produce a OS X version.
Good luck!