How do I make all the posts on the main page say leave a comment. Some of them do and some do not. Why is that?

I would need to see your Atahualpa settings. It looks like it could have to do with excerpts. What code have you changed in CSS Inserts or elswhere?

you have several threads going and some maybe causing others. in the case of 'Trying to change footer' (http://forum.bytesforall.com/showthread.php?t=7363) you only wanted 'leave a comment' to show and I suggested changing the footer to %comments('Leave a comment', '', '', '')%

If you read the documentation for %comment you will see that there are 4 parameters

%comments('No comments', '1 comment', '% comments', 'Comments closed')% - Displays a link to the comment section of the post. The link text depends on the comment count & status (open/closed).

When using this item, provide 4 text strings for the 4 possible comment states:
Replace 'No Comments' with your link text for posts that have no comments yet
Replace '1 comment' with your text for posts with 1 comment
Replace '% comments' with your text for posts with 2 or more comments. The % (percent) character will be replaced with the comment count. Use that character in your own text, too, unless you do not want to display the comment count.
Replace 'Comments closed' with your text for posts where comments are closed. Replace 'Comments closed' with 'dontshow' to display nothing if comments are closed (instead of displaying something like 'Comments closed')

so if you implimented my suggestion, you would only see the 'leave a comment' if there were no comments, I should have said %comments('Leave a comment', 'Leave a comment', 'Leave a comment', 'Comments closed')% (if you leave out the last one, then when the comments are closed, you will get nothing.

So now the question is: Did you make this change or is this a different issue?

when you run into a problem, keep track of what you are doing to fix it and tackle one thing at a time.