Moodle version 1.6:
Administration -> Configuration -> Filters
Filter match once per page
Automatic linking filters will only generate a single link for the first matching text instance found on the complete page. All others are ignored.
Filter match once per text
Automatic linking filters will only generate a single link for the first matching text instance found in each item of text (e.g., resource, block) on the page. All others are ignored. This setting is ignored if the one per page setting is yes.
Thanks for your help Joseph I wasn't aware of that feature. I tried matching once per page and once per text both individually and together and curiously the problem was been solved for most of the resources but persists for some!. Now, and don't ask me why, all of the resources are autolinked once. Thanks again.