I am using PHPed and debugging a local copy of the website. I can get the debugger to work, but I believe the error I am looking for is in a function in an include file. I can single step through the code that includes the file, but when I get to the function call, even though I click on "Step into", it just skips the line and ends the script, even though there are additional lines of code that are not executed.

How do I step into a function? As an aside, why am I not able to step through the rest of the script?

you may want to check ERRORS tab in PhpED to see what the error happened.
it's either a kind of function is not found or function is called with wrong number of arguments.