When roofing nails pop up it can be because the nails were not being held by the sheathing either because it is soft or rotten, or the nail heads were to small or possible the shanks were to smooth.
When installing roofing nails you should always make sure that they are nailed through the roof sheathing. Another cause is the temperature of the house, which is constantly changing and this can cause the nails to get loose and just simply pop out of the wood.
The different temperature of your house causes your roof to either shrink or expand and this can cause the nails to become loose and just start popping up out of their holes.
For roofing nails that pop up you should first check to see whether they have in fact penetrated the sheathing and if this is the case you can paste some roofing cement onto the popped up nails at the point where it has entered the roof and then hammer it back in place.
This will seal the hole when you hammer the nail back in place and then you will have to paste some more roofing cement onto the nail head to ensure that it is holding strong and will not be able to pop up again.
If you notice that your shingles are buckling or that they have become wavy, either running in a straight line up, or across the roof, this can be caused by improper nailing, and it is a sure sign that some of your nails have already popped up causing this effect.
Also deck or felt movement caused by the different levels of moisture in the materials used under the shingles will cause the nails to shift according to the movement of the deck.
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