I know what you are talking about. I have never been able to fully believe what I am seeing when it comes to the forces Simulation reports on bolts that I have added to a study. In my experience, usually not much more than the recommended preload causes the bolt to fail according to Simulation's Bolt Check. I am still using Simulation 2010 so am not sure if this has been improved upon in either 2011 or 2012. At this point I really only use bolts in my analysis to simulation the contact or grounding situation I am looking for and rely on good old hand calculations to determine bolt strength. Maybe someone else will be able to offer up more information on this.
You can get these results from SW Motion. Probably better results, actually. Model bolts as really stiff springs (with a touch of dampening) and get resultant deflections.