When cutting circles that are over three inches thick, I've found that angular lead-in's and lead out's seem to work better than the radius ones that we commonly use on thinner material.   I approach the material head on to lead in, (imagine cutting a capital "G" backwards) and leave at a 45 degree angle to lead out (like the tail on a capital "Q").
Has anyone else any better results with different configurations?

With all my cutting I use a line in / line out for all interior geometry and at corner on the line for the outside cut if the geometry allows it, if not I would use the line in line out. In this case with 3 inch material my line lead in would be set at .325 and my line lead out would be set at .05 and the at corner would be set at .325 lead in and .100 for the lead out. In the li/lo properties box the lead in angle is set at zero and the lead out is set at a 5 degree angle. 

Most definitely. I don't use the radius lead ins/outs on anything anymore...maybe really thin materials. As long as you have to box checked that does not apply offset to lead ins/outs, the lines work better than the arcs...and especially on thick stuff.

I was wondering about that checkbox.  If I don't apply the offset to the leads, will that keep it from leaving that annoying bump on the edge of the piece?  Or would it make it worse?

Yes, turning off the offset for a line lead removes the little bump.