I have heard about some rumors that there are / were bugs with header() calls. I don't know what's the current situation. You can probably find something in the bug database. Or if not, you can submit one new bug ;)
Right, I filed it as bug #24177.
As a temporary workaround for everyone that wants to use Apache 2, remove the call to flush() on line 31 in /include/do-download.inc (and don't forget to exclude the file when rsync:ing).
Huh. Does flush() affects this header behaviour? Strange...
Goba