@thomthom said:

I see this from time to time. Usually it's a result of using imported geometry from for instance DWG/DXF files with some minor precision problems that appear to cascade throughout the model.

Maybe CleanUp: http://sketchucation.com/forums/viewtopic.php?t=22920
But it won't prevent the problem from re-appearing. The root cause if probably precision problems.

Use imported geometry as a guide, but don't model directly off it. Don't trust it to be square or parallel.

Thank you so much for the input Thomthom. This is actually quite helpful. ^.^