Overall this is a very nice plugin. I've found it quite easy to customize. The main glitch I've run into is that I need to use it in conjunction with another plugin (s2Member) for advanced file permissions.
Each time you sync, the options for controlling file permissions overwrite whatever customizations you might have added in the .htaccess file. If you choose "Protect upload path" it puts it's own .htaccess file there (and will overwrite any changes you make at each sync). If you uncheck that option it deletes your .htaccess file on each sync.
The workaround I finally came up with was just to hack the /classes/Setup.php file and disable the UnProtectUploadPath() function. Will have to remember to do that again on any upgrades...