I am using SW2014 SP5.
I have noticed that if you create a Tapped Hole (ANSI Inch or ANSI Metric) and set the end conditions to "Through All" for the drilling and Blind (2 * DIA) for the thread depth the diameter of the threaded portion of the hole will be incorrect. I have figured out a work-around that seems to correct the issue consistently.
When the end condition is set to "Through All" the default setting for thread depth is also set to "Through All". Manually changing the thread depth to Blind (2 * DIA) causes the diameter of the threaded section to "remember" some previous setting. For a while I had #6-32 holes with 2" diameter threads. Now I have #6-32 holes with .06" diameter threads. The second sketch of the hole wizard feature shows the correct dimension for the hole specified, but the actual size created does NOT match the dimension and no amount of rebuilding corrects the problem.
The work around is to edit the hole wizard feature, check the "Show custom sizing" box under "Hole Specifications" and then change the default "tap drill diameter" dimension to anything else (remember the default setting). Click the green check on the hole wizard property manager. Next, re-edit the hole wizard feature and change the "tap drill diameter" dimension back to its correct setting. This seems to force a proper rebuild and the feature builds correctly.
I have attached a sample file showing the issue. I would be interested in hearing of other have seen this issue or if they even see it with my file on their machine.
I hope this helps ease some frustration for others.