In 2010 and 2011 professional, I am having issues with the Hole Wizard. We use server copies that are controlled by a government agency and the issue may be how/where they store the wizard.
Here's the problem:
After cutting holes in an assembly and exiting the function, the holes will randomly decide to disappear. This can sometimes be resolved by closing the assembly or SolidWorks. They may reappear or they may stay lost. It may be some or all of the holes I cut.