From the perspective of php.net itself, it seems like a false positive:
It turned out that by combing through the access logs for static.php.net it was periodically serving up userprefs.js with the wrong content length and then reverting back to the right size after a few minutes. This is due to an rsync cron job. So the file was being modified locally and reverted. Google's crawler caught one of these small windows where the wrong file was being served, but of course, when we looked at it manually it looked fine. So more confusion.
We are still investigating how someone caused that file to be changed, but in the meantime we have migrated www/static to new clean servers. The highest priority is obviously the source code integrity and after a quick:
git fsck --no-reflog --full --strict
on all our repos plus manually checking the md5sums of the PHP distribution files we see no evidence that the PHP code has been compromised. We have a mirror of our git repos on github.com and we will manually check git commits as well and have a full post-mortem on the intrusion when we have a clearer picture of what happened.