Vertical holes too small

I am having problems with vertical circular holes printing too small (this includes polyholes such as those on the Prusa parts). Other dimensions seem to be OK. Even enabling Slic3r's hole size compensation and rebuilding from source doesn't fix the problem. The one thing that I have tried that fixed it is decreasing the extrusion multiplier, but that throws off the other other dimensions and weakens prints. Both ABS and PLA prints seem to be affected. I am not quite sure how to fix this other than either modifying Slic3r's hole compensation to compensate more or possibly trying to switch to Skeinforge for parts with vertical circular holes.

I am using a recent version of Slic3r from git. My printer is a MakerGear Prusa. I have attached my Slic3r configuration for ABS.

Have you tried with a different slicer (like Skeinforge or Cura) to see if it's Slic3r or your machine?

Have you printed any height calibration parts to confirm that your printer is getting the right height?

Do other vertical components on a model print out the correct height?

I had issues with objects being slightly compressed in the Z due to my Z value in the firmware being slightly out. Also, skipping steps in Z will lead to height shortfalls.