flow timeout v2.2

Fixes unix socket runmode, otherwise the same as https://github.com/inliniac/suricata/pull/1267

Prscript:
- PR build: https://buildbot.openinfosecfoundation.org/builders/inliniac/builds/95
- PR pcaps: https://buildbot.openinfosecfoundation.org/builders/inliniac-pcap/builds/95