Finally had a chance to look at this ...

Netfabb Basic is not able to make complete repairs, so I tried Average Weld on vertices in Hexagon and then brought it back in to Netfabb Basic but it did not help much.

Did you model this totally in Sketchup?

Boolean operations I suspect are the contributing problem here. There's usually some very small error involved that when the retriangulation is performed, triangle(s) may be created where there should not be any (such as covering a hole that was created by subtracting a cylinder, where the end of the cylinder is on the same plane as the hole)

Before I had Netfabb Pro, I did all my booleans in Hexagon and used Avg Weld, and prior to going through Netfabb basic. I also had to ensure that there were no Ngons or quads prior to using a boolean operation (in other words, use fully triangulated objects).

Its hard to say here what exactly is happening without doing some tests.

One thing to try is building your objects 100 times larger, prior to doing any booleans. Some modeling applications don't allow you to increase the decimal accuracy, so multiplying by 100 gives you a couple extra decimal places to work with.