I am not using the module positions 28-31 and 5, why is it leaving a large gap on my home page? How can I remove it?
There is a gap there because there is nothing displayed in the position. Your positions do not collapse if that is what you are asking. You can edit your module code to get rid of the space if you need. :)
That sounds like a badly-coded template to me. Unused module positions should automatically hide?
Can I ask which template you're using?
You can edit the template module positions by going into your /templates/ folder although I'd suggest taking our Template Design class before doing that are there are several steps involved in making a module hide automatically: www.ostraining.com/courses/class/joomla-25/j25-templates