I am using repetier-host with RAMPS 1.4 and Marlin 1.1.0-rc7 Something weird is happening

I am using repetier-host with RAMPS 1.4 and Marlin 1.1.0-rc7

Something weird is happening with the extrusion rates. If I boot the ramps, then go straight to a serial connection and issue

G92 E0
G1 E100

Out comes 100mm of filament. So I know the steps are right.

Then if I fire up repetier-host, and extrude 100mm, out comes around 50-54mm

I can see that it G91 switches to relative, then G90 back to absolute, but still, if I issue the commands above from within repetier-host, I get half what I expect (this is without the hotend).

I checked the eeprom settings that repetier host sees, and the the extruder steps per unit match what I upload from arduino-ide

I have a problem with severe under extrusion, so I am wondering if this is what is causing the problem, or it is just how it works.

Repetier-host was downloaded about a month ago, so pretty new.

Is there a setting somewhere that overrides what the steps setting is that I am missing?

Are you over driving the stepper’s speed and skipping steps? Check the speed settings in Printer Settings.

In repetier I have the manual slow speed at 2mm/s and fast at 20mm/s, the default I think

At both speeds, about half comes out

I guess I need to log the command sequence repetier sends and step through them one by one on a serial connection to see what happens