Downloaded older 1113 version from here:
http://skystrife.com/x264/x264.1113M.x86.exe
Renamed it to x264.exe and replaced the one in the C:\Program Files\MeGUI\Tools\x264\ directory ran the same queued jobs and they seem to be working fine. Won't know for sure until encoding finishes, but looks like there is an issue with version 1114 and MeGUI of some kind.