Paging filter doesn't act on previous filter output

Hi, I'm totally new to this stuff so I hope this question isn't just stupid. :)

I'm using default paging separator, the correct node type, and an input type that includes only a customer filter set (Custom Filter module, weight zero) and Paging (which is last, weight 10). One of the custom filters inserts the paging separator based on a regex match.

I /thought/ that because paging came later in the input filter, it would then see the paging separator tags inserted by the previous custom filter, but it does not. It only sees the separator tags that were explicitly placed in the original document.

Is this the way it's supposed to work?

BTW, I also see the "<!--paging_filter-->" getting output to the browser, as was mentioned in a previous post.