In the options you can set 'Cancel Skip/Auto Mode for phone triggers'. But this should be on by default. This worked perfectly for me.
Maybe you are using 'forced skip' instead of the regular skip? In case this makes any difference.
I was using regular skip yes, it stopped doing it now, I think I'm going crazy .
Where did you read that the vita version had issues? AFAIK it doesn't.
But yeah, skip with Start, not R.
I read there were parsing issues (which I'm also experiencing). So I thought there might be more that's a little bit off. Think I read it on the first few pages of this thread (or another thread on GAF)?
Man, selecting the right options for the right paths is always such a hassle in VN's, time for Faris's route though.
Edit: Also this has to be mentioned at the top of the page (to make my post a little less shit); the voice acting in this game is amazing.