Print job won't start, hot-end not heating

I have a bit of a problem: When I try to start a print, the hot end won't heat up, and none of the axes will move. The bed heats up fine.
The thing is, I can heat it up perfectly fine if I do it manually, and all of the axes move correctly, when done manually. Only not when actually printing.

I'm using Pronterface and Marling firmware on a RAMPS board. I also tried Repetier. When I use Repetier, it seems to set a target temp, I think, but not in Pronterface.
It seems likely to be a firmware problem, I just don't know what. Any ideas would be much appreciated!

I can also add, that I have managed to print before, but I had a issues extruding, so I got a new and better hot-end. I don't remember changing anything other than that.

You didn't say what printer you are using, but I know that with my Prusa i3 if I just click the print button and let it do everything on its own it will spend a lot of time heating the bed and not the hot end. But once the bed is hot it will heat the hot end. The hot end heats up much faster than the bed. Also, it says it is heating the extruder the entire time even though that is obviously not the case.

Open up the g-code file in a text editor and look for M109 - this is the command to set the extruder temperature and wait for it to be reached, before printing starts. If there's a problem, it's probably around there. What might be happening is that the printer is trying to set the bed temperature, not getting to the set temperature and not getting beyond the M190 command, which sets the bed temperature.

You could send an M31 command to the printer while it's stalled - this outputs the time since the last M109 command and will tell you whether the printer reaches the M109 command in the g-code.

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