The difference is for programs like this:

#!/usr/bin/perl

## uncomment this: ## $|++;
print "content-type: text/plain\n\n";
system "date";
[download]

When left commented, this fails (under both apache 1 and 2) because the system date comes out before the header, causing a 500 error.

When uncommented, it works correctly.

This is what I'm talking about. You were probably testing something else, like whether you could see it all the way through to the browser. That's a different problem, and was never related to my use of $|++.