What does the code snippet do? I was having conflicts

I have a site that is structured like so:

Primary Link 1
- PL1 Child 1
- PL2 Child 2
- PL2 Child 3
Primary Link 2
Primary Link 3

I have the first level of the primary menu across the top. I have the child level on the left. When on any of the child pages, the name of that page would be highlighted as would the parent. (Attachment 1)

But in some cases the Child would forget it's Parent (Attachment 2). I checked the menu table to be sure that the pid (parent ID) was set correctly. It was. I couldn't find a pattern.

I then tried to deactivate the Menu Trails module. When I did, I got a white screen and checked my log. I got an error that it couldn't find menutrails_primary_links(). I checked the install documentation (README.txt) and recalled adding the function to my template.php file. I commented it out and then I no longer got the white screen error. Note that I am using Zen theme and it requests that varaibles be added by a series of pre-process functions, so my code looked like this:

function mytheme_preprocess_page(&$vars) {
	$vars['primary_links'] = menutrails_primary_links(1);
	$vars['secondary_links'] = menutrails_primary_links(1);
}

After commenting the two lines above, the site loaded and I was no longer having a problem with parent highlighting disappearing. It's not clear to me why we need to add those two variables.