Is it only the base? I have an issue in slic3r where the bottom layer does not extrude at all. The extruder motor never even turns.It did take me a while to figure it out, since it would extrude a little bit each time it did a retract (on a fast move), resulting in very little amounts of filament being laid down.
I don't know why, but it's not that big of a deal. I usually open the gcode in a text editor and just delete the first layer, and copy/paste the second layer in its place.