staining shiplap board

I recently cut to size shiplap boards made from eastern white pine and purchased from Home Depot. I've begun staining three of the boards and have found that two of the three have what my brother calls "chatter" on them. Essentially, the two boards look as if the stain has a "skipping" effect to it all along the length of the boards. One of the three boards looks just fine.

Here is a photo of the boards: http://imgur.com/BRJkaO8

You can see that the boards on the left and right have the skipping effect while the board in the center looks normal. I have stopped the staining process until I can determine what is the best course of action. I do not like this chatter and would like to repair it if possible on the two of these three boards and I would like to ensure the other boards I have to stain do not end up like these two.

Is there a course of action you might recommend? I thought I might try sanding them with a 4 inch, electric palm sander. My brother suggested doing it manually with a piece of hard wood blocking with sand paper attached to it. Of course, the electric process sounds more appealing to me. I asked about a belt sander, but I'm told this will likely leave long wave-like marks in the wood.

Maybe there's some sort of primer or chemical I could use?

Maybe the chatter will just disappear when I add the second coat of stain?

If it matters, I intend to apply a satin polyurethane to the boards once they are stained.

I'd appreciate any advice.

Thank you.