I just did the ver .47.2 to ver .47.3 update.
The .htaccess file permission was changed during the update to unlock the file. It does not automatically re-lock.
The recommended permission is 404
If you don't use the "edit/upload/download" tab feature to re-lock, the permission will be 644
I noted this here in the support forums for the last release, too. I thought you had indicated that it would be fixed - just wanted to make sure you are aware that it's stilling doing that.
Again, thanks for the great plugin! :-)