“I am going into a Sony XDCam R1 deck and it gives me a reference error every so often and the video goes to black.”
I don’t think this is a Premiere problem. I think this a deck sync problem. I may have a solution or I may not.
Your deck’s input should be set so that reference should be INPUT VIDEO. Anything else and it might be trying to reference to sync that it can’t find. (like an external clock or sync pulse generator) This is true of all pro/broadcast VTRs and may well be true of your XDCam VTR.
You need to make sure that the deck takes its sync from your input video not look for it elsewhere.
You might also hear the VTR servo struggling to look for sync as it records and this is a tell-tale sign of no proper reference signal.