with 2010, yes most of the time the countersunk holes are shallow for me. counterbored seem to be fine. I catch it most of the time and when I don't the machinest comes to remind me.
This also depends on the fastener manufacturers that you use, though there are standards that can be found in Machinery's Handbook etc.
Once you find the setting that works best for the hardware that you use, you can make favorites in the hole wizard database and use those. Not exactly an answer to you question but a general tip to avoid the intern issues in the future. Just have to show them where to get the favorites and how to use them.
I had a big problem with the countersinks being the wrong depth until I noticed that there are are both "counter-sink" and "socket-head counter-sink", and they are two different depths.
Once I started using the correct hole callout (SolidWorks has both) for the correct size screw everything came out better.