I just had about 900 square foot of apx. 1/2" engineered hardwood (mirbeau weng) installed and the flooring nailer (http://images.harborfreight.com/manuals ... /99640.pdf) left these marks where the feet of the nailer touch the edge of the wood flooring above the tongue. The mark looks like a surface crack semi circle to the left or right of where the cleat enters the wood. Has anyone ever heard of this or know what can be done to prevent it? I may resort to glue down but would prefer to nail. The floor is going down over 3/4" wood subfloor with rosin paper. Any help greatly appreciated!

Well, I am going to assume you put the 1/2 inch adaptor plate on the machine before using it.
The marks you describe generally come from an inexperienced user who has neglected to seat the plate of the gun squarely on the edge of the floor; thus creating an impact point at the edge of the stapler.
Also, I am a bit concerned that the 16 gauge (actually, 15.5) is too heavy for a lot of these 1/2 inch engineered products and may show up as dimples in the surface of the floor in certain light conditions.

Yes, the 1/2" plate was installed. I was just looking at the product info sheet and it says the flooring is 9/16", not 1/2" as I thought. Could this lead to problems? I'm not sure if the problem is that the gun was not square. Although I did not do the install, the installer has done many flooring jobs before. Do you recommend going with 1/2' x 1.5" crown staples instead of the cleats? I plan on doing some tests on scrap flooring to see if the gun was out held out of square or not. I was not on site during the install so I didn't actually see him nailing it. I can tell you that there are many many many of those marks. Ughhh.

There's your problem, using a 1/2" plate for 9/16" thickness. The gun isn't seated securely, and I'm guessing not shooting the fastener exactly at the crease, at the top of the tongue. In that situation you can use a shim to seat the gun properly.

You may want to consider using 15 lb. saturated felt (roofing paper) for your underlayment, instead of red rosen. IMO red rosen is used as a cover paper to protect the floor after installation.