What makes Pronterface wait for user? I'm using Cura with the Pronterface UI to slice/print and sometimes printing just stops - always in the first layer - when it happens the printing screen shows "Waiting for user", when I press the button on the printer printing resumes.

I don't know when this happens, it just happens about once every 5-10 prints, when this happens if I close the printing window and immediately click "print to usb" to reopen it the problem doesn't repeat.

This only happens with the Pronterface UI, it doesn't happen with Cura basic UI or when printing using an SD card.

Not using Pronterface isn't a good option because when I'm fine-tuning a model it much more convenient to send a test print from the computer and not copy the gcode to an SD card and print from the printer.

My printer is Robo3D R1+
That's the temperature problem that you've encountered.

The temperature of bed and hotend is reported every few seconds. Per default, first that sets is the bed temperature, then you need to wait for the bed to reach it, then warm up the hotend, and then start printing.