I would first try to remove the Wine trough apt, along with all of it's configuration files:
apt-get remove --purge wine
Then add the reposity from wineHQ and reinstall Wine with apt or Synaptic (instructions there - basically copy+paste two commands). If it still doesn't work, you should maybe post some error messages here to give a better picture of what's happening..
I have seen only one Wine installation so far that doesn't run anything except for winecfg, and removing/purging/reinstalling it doesn't seem to help at all. So it is possible that the reason is more complex than just some configuration file..