The printer has a filament center built in and it definitely works for gcode running on the printer itself. 
I have Repetier-server 1.4.4 running on a pi. The filament sensor definitely sees that the filament has run out but the job does not stop when the Gcode comes through this device. The printer just continues to print.
Is Repetier server doing something to disable this built-in printer functionality? Or do I just have something not set up correct??
I've been very happy with Repetier for about a decade and I'd hate to move off because of this.