print stops at M109 in g-code

I've been printing a lot with my Prusa i3 but suddenly I got this strange behaviour.
The print stops after the initial start G-code, like heating up the bed and nozzle and also the "Custom Start G-code", including G29.
It looks like the program is waiting for the nozzle to get to it's chosen temperature even though it already reached that level.
The behaviour started a while after I activated auto bed levelling.

If I edit the g-code and set the first nozzle temp command, M104, to 5 degrees lower than the later M109 it will continue the printing as normal.
Can the PID settings have any influence on this? I did a "PID Autotune" before this behaviour arose. I can't understand how it could make this happen though.

Marlin version: 1.1.0-RC5
Printrun version: 2015.03.10
Slic3r version: 1.2.9

Grateful for any help make me understand this behaviour.

Edited 1 time(s). Last edit at 05/17/2016 02:27AM by kakbit.

After changing from Printrun and Slic3r to Octoprint and CuraEngine the I have no problem with stopped print jobs any more.
I'm not sure if it has to do with the change of programs or if it is because the different gcode init that CuraEngine is creating.
It is working good now and I actually like the new setup.