I'm quite sure it's hardwood rubbing at joint. The strange thing is when I finish a row, they are very good by testing. But after the next row is finished, one or two joints of previous row may squeak. Now I have almost finished entire the first room. Many joints have this problem. I have #15 felt paper underneath. My subfloor is not very flat but not too bad. For some boards, I put extra very small #30 felt paper pieces. I use the Bostitch Manual Hardwood Flooring Nailer, so I use a lot of strength to hit. Is it possible when hitting very strongly, the new row has impact to the previous row and make that joint loose a bit?
Another possible reason I came up with is the nails are too close to the end joints. I had 1" at beginning and 1.5" later. The production manual suggest 1"-3" at minimum.
Here suggest 3" at minimum.
http://www.hardwoodinstaller.com/har...s-quantity.htm

What species of wood? Thickness and type of underlayment under the wood flooring...ply or osb or particle?

Moisture content? Pressure using and depth of fastener? Oh sorry you said manual? How deep is fastener going?

What do you mean by "testing'? You could be slpitting the tongue on the ends. I never go 1 inch.

3-1/4"W 3/4"T random length red and white oak
subfloor is 3/4" plywood T&G.
I don't have regular 1/4" plywood underlayment.
I just put #15 felt paper. For some low area, I put #30 felt or shingles under #15 felt. When installing, if I feel gap between the board bottom and #15 felt, I may put extra #15 or #30 small pieces.
I don't have data of wood moisture. I just have a environment humidity meter. It's 60%-70% in evening and night. Should be lower in the afternoon. My planks were also acclimated in such environment.
2" fastener, It's a manual flooring nailer, no pressure adjustment, I just hit the nail to the deep the tool required.
The testing means I stepped or walked on it. 1" maybe too close to ends, but no tongue has splited so. I'll try 2" tonight.

Sounds like you may have movement as a result of trying to flatten the subfloor, with scraps & odds & ends.

Actually boards on shingles & #30 felt have less squeak. I see 50% squeak occouring on joints without tight seams. Maybe boards or my installation problem, I can't get a perfect seam for some boards. Is there anyway to prevent squeak?

You will need to determine whether it's squeeking at the fasteners or creaking at the seams. Either squeeking or creaking, something is moving or loose, not going in solid.

Well lets operate on one!

Here is my take on the problem. First, move those end nails out to about 3 inches from the joint.
But I think the problem can be at least partially analyized by your description of when the squeaks start occurring. When you have nailed a row down the fasteners are holding the entire row of boards tightly to the subfloor. When you nail the next row, squeaks develop in the previous row. Just a guess, but I think the groove of the new row of boards may be located just off line enough to be lifting the prior row just off the subfloor. Because the endjoints are always milled loosely, you now have some excess movement in the end joint that is causing the squeak.
Just a guess, correct me if Im wrong.

Didn't think about that. Easy way to tell is just dry lay some boards together, and see if the groove is lifting the tongue.

Both flooorologist and dennis have very reasonable analysis. Last night I nailed 3 rows. I had around 2.5" to end joints and spent more time to fix the flat problem. After I tapped a new board, I used a small piece of #15 or #30 felt to detect the bottom of the board. If I could insert the piece easily, just left it there. After I felt it could not move up and down slightly then I started to nail. Those 3 rows seemed better. I haven't got squeak. It looks if flat problem was fixed, it's not likely the groove lifting the tongue. Thank you guys! Not sure if I can use small pieces felt paper like that.

Nothing wrong with using felt paper to build up low subfloor spots on a naildown.

OK.