Do you have faces that won’t print?
Your problem has to do with faces in the model being reversed in SketchUp, or corrupted when saved. Its something that wasn't an issue with ReplicatorG, but had become one in MakerWare. Which is why you often see this problem with older models on Thingiverse.
There are three possible fixes for this.
1) (If using SketchUp) Go back to your SketchUp file and check the bad faces. You may need to delete the face and redraw it, or sometimes simply clicking on it works. You also see this “grey out” effect on faces that did not select properly when saved and “re-saving” may solve it.
(a) Remove any "paint effect" if you have used it on your model, this will cause confusion about whether the faces are correctly oriented.
(b) You can repair miss-aligned faces by selecting a face you know is not properly oriented and right click. Under the right click menu select 'Orient Faces'. The Orient Faces command will make all of the faces in that object match the orientation of the face you selected.
(c) You should also remove any unnecessary lines that are cutting a flat face into pieces so that the face becomes one, instead of hundreds.
2) Repair the model using Netfabb Cloud services. You can upload the non-working stl file to the free service, and it will make a best guess attempt at fixing it. It usually very good at fixing this type of problem. Here is a link to the service: http://cloud.netfabb.com/
3) Use Skeinforge instead of MakerBot Slicer (by selecting “high” resolution). The problem you're experiencing could be a MakerBot Slicer bug. MakerWare still uses Skeinforge to do high quality prints. In the 'Make It' dialog box select 'High Quality', then change the layer height from .1mm to the layer height you want.