Pages showing as Archives after using Loop

Hi Guys, long time user and reader of the forum but this is my first post. In short my problem is that I am using a custm page template for my home page, and inside that template I call 3 loops and 1 query. They execute fine, but when viewing my breadcrmb it shows the front page as being the Blog Category page? I added a short PHP echo with is_archive() and it returns true!

How do I get to have the loops but without turning the page into an Archive?

This also affects the Author page which is author.php and which outputs the basic info of the author along with a loop of the last 3 posts by that author. Currently this page ignores is_author() but responds to is_archive() – I would like to get it to respond only to is_author()

For security sake I can’t post the actual URL here but this shortlink will get you there:

http://goo.gl/O0tMs

Here is the code of the Home Page template (please excuse my god-awful hacking!):

[large chunk of code moderated – please use the http://pastebin.com/ for any code longer than 10 lines – see http://codex.wordpress.org/Forum_Welcome#Posting_Code ]