The only times I’ve heard of any problem with this, it was related to permissions–partly because its no longer the appropriate place for a preference file. When it occurs, it would be interesting to take a look to see if the file is still there, and then if the user can open it in, say, TextEdit.app.
If its a real nuisance, you might want to submit a proper support request. They may have more in-depth troubleshooting options and able to tell you if there are any related outstanding bugs.
Another important point is that the Native Client is not yet supported under Mac OS X 10.8. They would like for it to work, so if that’s the case, there must be significant outstanding issues. Are you using 10.6 or 10.7? That situation is a little painful, but I don’t know what percentage of users are still using the Native Client. Perhaps those that are tend to be more conservative about their Mac upgrades as well.