I just thougth I'd post a reply to update what I did (incase anyone was wondering):
UPDATE: I've ignored the problem
Actually, I worked around the problem. The file center works fine for "normal" JPGs and GIFs but just not these thin and long GIFs. So I worked around the problem by NOT uploading these GIFs into the file center.
I didn't really need to anyway because they were part of the template. So I simply put the GIFs in the pictures folder and linked to them from the HTML img tag as normal.
So the problem isn't solved - I've just ignored it and put it off until next time