Gang, I have finished thousands of board feet of cherry in my life but I have a new one that I need help with.  I’m building a custom cherry flag case for a customer in Colorado and when I began to apply the finish I saw these staining streaks on it.  It is Pennsylvania cherry (sorry Lew) and I am stymied.  It isn’t a result of the machining process because I was planing three pieces and this is the only culprit.  Any ideas?

looks like the grain is not pretty on that piece.

I was thinking similar to @DAB. That area looks like a transition between the direction of grain patterns.

It does. I am remaking the top triangle this afternoon.  A real bummer because all of the corners were very tight on this one. 

Almost looks like some spalting or punkiness before it was dried. 

I am with Grandpa , looks like early stages of spalt. I use Garnet Shellac to even the color out in cherry , which can have some unique color variances.

Typically, I will apply a coat of Zinsser Seal Coal on cherry before the finish coats of General Finish Arm R Seal.