I have pushed out a small fix for the configuration file (./app/config/config.php) out to all versions of MiniMVC. There was an issue that if you put MiniMVC a few folders deep the URLs would start losing folders. This has been fixed as well as I added a / at the end of the index.php so that it too can be used properly (i.e. not a special case to be handled differently than if __SHOWINDEX__ was disabled).
Sorry for any inconveniences these bugs may have caused.