This has to deal with using meta_keys to list your posts and conditional tags in a index.php and category template file.
In this example in the index.php I was using:
query_posts('meta_key=your_first_meta_key_name'); $i = 1;
then in the category(-*).php file I had to use:
query_posts("category_name=your_category_name&meta_key=your_second_meta_key_name"); $i = 1;
instead of:
query_posts("meta_key=your_second_meta_key_name"); $i = 1;
Otherwise it would ignore the is_category('your_category_name'), is_category('#') and is_category('Your category name') conditional tags, and instead only listen to the is_home() or is_front_page() conditional tags, if these conditional tags are present in the category(-*).php template file.