Repetier Host currently comes with Slic3r 0.9.7 and Skeinforge 50 bundled with it. Skeinforge 50 is a bit different from Skeinforge 39, which comes in the Solidoodle download. The main difference is that it calculates flow rates automatically, much like Slic3r.
The settings for this are in the Dimension tab.
Measure the filament in several places with a caliper and enter the average in Filament Diameter. Filament Packing Density is like Slic3r’s extrusion multiplier, but in reverse. Higher values mean less flow. I’ve found that 1.18 gives me accurate thread widths, based on the extruder being set to 109 steps/mm in firmware. Start here, and find a value that works for you based on the test in Setting the Flow Rate.
Even though the flow rate is now handled by the Dimension tab, the Flow Rate setting remains in the Speed tab. Set the Flow Rate to the same value you are using in Feed Rate.
Be careful about switching back and forth between Skeinforge 50 in Repetier, and Skeinforge 39 in Pronterface. Both of them keep the current settings in the same place. If you have Feed and Flow both set to 50 for Skeinforge 50, they will both still be 50 when you open Skeinforge 39 and you will have to change the flow rate back to its original value. And in reverse, when you go back to Repetier and Skeinforge 50, if you don’t change the Flow Rate back to 50, you will barely get any extrusion.