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.