You have an issue in your install, since all WMV3 files play on latest 08.6c on my mac.
Okay. I ran the delete prefs script and put my VLC folder in the trash. Did a manual seach to make sure all the VLC related files were in the trash and deleted all of it. Restarted the comp and re-downloaded the latest build for Intel, same as I was using before, 08.6f, still won't play the video portion of the files showing the same error. Did the deleteing and re-installing again with 08.6c like you have and got the exact same results.
Thats as far as I'm going with this. Not going to do a fresh OS X install since I have had no problems with other programs and like I said, VLC plays 90% of files properly, this is the first time it has shown this error with a video file. Only problems are this WMV3 thing and VLC tends to have problems with displaying A-S-S subtitles correctly more often than not.
My comp is a '07 Intel Mac Pro running OS X 10.4.11, if that helps at all.