I have a super generic Reprap Prusa I3, with Mega and Ramps 1.4.
I have been using Repetier Host and firmware 0.83 for a while with no issues.
Then I bought a "Reprap Discount Full Graphic Smart Controller" to allow printing detached from my computer.

The latest repetier firmware says it works with that lcd screen, so I tried.
It all works, except I noticed the extruder cannot be manually moved using host, though the lcd controller can move it using the dial.
I tried a test print and the extruder does not move.
So I then tried many things.
I put old firmware (0.83) back on and the extruder works.

I unplugged the lcd board and configured firmware to not use it. Same problem, no manual extrusion
So it seems to be a general config problem. Not the host.
I even replicated on another host software so I know it the 0.91 firmware (and its config).

I then carefully compared my configuration.h from old and new firmware, as well as pins.h.
I will mention that I put my x axis motor on extruder2 slot on ramps, and modified pins.h to accommodate, but I have had no issues with that.

Having gone through the config at least 10 times, and trying many things, I cannot get the extruder (only one), to be recognized.
The extruder heater works fine.

How in the world could the LCD be able to run the extruder motor, and not the host?
I am about ready to give up repetier firmware.

So I tried switching to marlin firmware, as it supports the FGSC lcd thing.
I noticed when I tried manually moving the extruder, I got some message like "cold extruder ignored...".
So I preheated the extruder, and then it worked.
I then switched firmware back to Repetier and same trick worked.

This means I fooled myself on the part about the extruder not working during a part print.
I think what happened was there was another issue I had forgotten I fixed, after the test.
If I had tried again, it would have worked.

Moral of the story - There should be a big red warning that manual movement of the extruder is disabled due to temperature.
Why? Because anyone doing dry runs and setting up a machine will run things without filament, and will not think to heat anything.
This took me two weeks of tinkering to figure out. Not constantly, but here and there.
I might switch to marline now, as the lcd screen is nicer IMO, and the motors ran quieter for some reason.