The bottom line is Moodle 2 is going through some 'growing pains' and there is some 'discussion' concerning how the new version (2) handles files.  This page will reference some and are worth reading IF you have version 1.9.x and are contemplating the move to 2.x. (remember, the option your MoodleMaster may choose is to migrate the entire site - once done [if there is no backup to restore to a 1.9.x flavor] there is no going back ... period!).

IF you've already made the jump, maybe this information will provide some clarity.

Discussons: Repositories
http://moodle.org/mod/forum/view.php?id=1807

and in another:
http://moodle.org/mod/forum/discuss.php?d=174702

A slide show worth seeing … all 80+ slides (might get you ready for the number of questions you will, as 'MoodleMaster', be getting).  Hopefully, however, you won't be giving the 'Dave' answers.