I have had this issue with several different models. Sometimes it seems that MatterSlice does not see the entire first layer of an object. For example these screen captures of this .stl:
http://www.decalsandtees.com/mattercontrol/phi.zip
http://www.decalsandtees.com/mattercontrol/matterslice.png
and compare it with the same object sliced with the Cura engine:
http://www.decalsandtees.com/mattercontrol/cura-engine.png
I am using MatterControl 1.1.2.2279 with a Printrbot Simple
MatterControl respects your First Layer Extrusion width setting. You probably have it set to 200% (the default). This is causing the first layer to have thicker lines than in CuraEngine. You can change it to 0 or 100% and it will be the same as CuraEngine.
Fantastic, I never even thought of that.
Thanks!