This is the first time I have had this issue, but the perch_pages_breadcrumbs() function isn't working in sub-directories. I'm presently applying it to /blog/index.php and I set up a test/index.php to see if it was any sub-directory(it is) to no avail. Works fine on all pages in the root directory.
I'm using debug on the page, but the function isn't even being called, neither the template listed nor any links on my page. This is strange. How can it be right and wrong at the same time.