DNS flood slowdown workaround, general TX handling fixes

See https://lists.openinfosecfoundation.org/pipermail/oisf-devel/2013-November/002783.html

Also, fix improper TX handling when loggers were disabled. The app layer api would still consider them present, confusing TX cleanup.

https://buildbot.suricata-ids.org/builders/inliniac/builds/47