Whenever I have loop record on it will offset the recordings, usually running a guitar track with Guitar rig 5 on, this is in both sound on sound mode and comping.....It also does it recording MIDI tracks as well.
Latest X3, Win 8....It only started when I installed X3e sometime ago.
My only workaround is to not record in looping mode which kinda defeats the object. i havent tried yet with a 2 bar count in yet tho, which I will try.