While wondering, which package(s) left that file over during emerge, this package is a good candidate.
This is a bigger problem affecting the eclass, but at least for this package, I just committed a new revision to avoid it. After we stabilize PEAR-HTTP_Header-1.2.1-r2 in a month or so, I'll remove the old version that uses the PEAR eclass and it won't have this problem any more.
The new eclass-less version is stable and the old one is gone.