I am having this same problem today, but with Studio One Artist 4.6. At the same time, my keyboard shortcuts stopped working. To initiate recording (once the track is armed) I have to click the actual RECORD button twice. S1 then records for a random period of time before it decides to stop recording, while head transport continues in playback mode. When I am reading a narration, I suddenly notice that I am no longer being recorded and I have to go back to the end of the recorded track to figure out where to pick up the reading again. I'm going to have to download the free version of Pro Tools just so I have a back up to my Presonus DAW, I guess!
I've already got a ticket created, but in checking the forum it doesn't seem there are any ideas as to how to fix this problem. I am using an Asus G75V i7 with 12 GB of RAM for my DAW, pair with a Tascam US-2x2 interface.