Is there a way to change (globally) settings for the way files are displayed etc within the 'Files' folder for each course within Moodle?

The problem we've discovered is when files are added individually to a Moodle course, they open fine (the files give the usuall Open, Save, Cancel box). If, however, a link is created to a folder within the 'Files' section, then a pop-up appears before the Open, Save etc. This is randomly creating problems as (I think) IE is blocking the pop-up and therefore not opening the file. Another problem with XLS files, is a login appears within the XLS file instead of the data that should be there.