I had to send a work crew home today: they laid three rows of hardwood (Sunca, 4" x 3/4" brazillian oak) using 2" cleats and with every cleat I can see a dimple above it. I can only see the dimples when I look down the board with the light striking it from the side, however in my house this is the norm. I have 30 foot runs of board, so it is an obvious defect that ruins the look of the floor.

I asked them to change to staples, so they did, and this did not help. I switched out the air compressor, which made no difference.

I am at a loss to know how to proceed. Should I try smaller staples, like the ones used on engineered wood floors? Should I ship 1000 square feet of this wood back to the supplier and ask for my money back? My house is in obvious disarray: any suggestions? Can I glue this floor down?

Could be a number of issues....Your not getting enough PSI to countersink the fasteners..and/or, the fasteners are not in the proper location,(the"crotch"), of the tongue. Could be pneumatic gun issues. Could be a fastener length and substrate combination issue.

I wouldn't recommend gluing. Especially wouldn't install 3/4 with "engineered staples"

Look at your directions for the floor they may call for 18 gage cleat. I know alot of exotic 3/4 inch do. You can rent powernailer model p50 at home depot and they sell 18 gage cleats. this may solve your issue it did for me on a brazillian walnut floor