hi patrick, did you use glue on some places? if so the glue make appear to be gone but some will be on the surface and will not let the stain soak in thus the streaking problem.
Hello Patrick, If I would have to guess, without seeing a sample of the wood, I would say that the most likely cause is the woods grain. The darker areas are because of the soft places with more of an open grain and the light places are the harder places caused by the grain being more closed.
It is a frequent occuring problem in hard woods where the wood grains are so tight that the stain will not penetrate into it and sometimes will just sit on the surface and even dry without penetrating. An example would be that of something like rock hard maple or hickory compared to that of alder or pine. The alder and pine being a more soft wood will except stain easier that the maple or hickory. This is particular noted in the plywoods with birch and other softer plywood being the biggest problem. In the soft woods is where I would suggest the use of a sanding sealer be applied prior to finish.
Before building a project and during my picking of my stock I have taken time to watch for troublesome lumber, not only for grain pattern and appearance. I have gone to the troubles of even taking hard wood solid stock and taking 4- o steel wood and rubbing the raw wood surface in a polishing effect. Then looking at it in a bright light and shinning the light across the surface looking I'm for a tell tale signs of a streaked effect, where there is higher shine than that of the larger surface. This sometimes reveals a surface that I know will not take stain as easily as the dull surface. I will then test that surface with some actual stain or even select a different piece of stock. I realize that you can't always do this especially at a lumber supply but once in the shop if you suspect a problem it is better to take the time to do this as it is just as important as the grain pattern. Taking the time in selection of the lumber of which will become visible in the finished project is worth every ounce of percaution you can take. After awhile you will gain the eye for spotting lumber that will yeild a troublesome project and it will become a thing you do with out thinking about it. Just as automatic as spotting a cupped, warped, or split in the stock.
I have had the experience of dark and light streaks in a project where the only way I have overcome this is to use a method I call tattooing the wood. This is where I take a very sharp needle and make a series of many needle punctures in the offending area. I do this with a coat of stain covering the area and repeatedly wipe it off until I get it colored as close to that of the surrouning area. I allow the stain to dry and then lightly buff it off. If it looks right then I seal it with a clear top coat. This has happened to me many times especially when refinishing something where I did not have the opportunity to pick my stock.
The apparatus I use is simple consisting of a something like flat stir stick for paint and insert a series of sewing needles through the surface until the needle point is exposed maybe 1/2 inch. Taking that in my hand i begin a series of controled tapping of the needle points on top of the offending area. What this does is makes a small crater for the stain to enter and dry. It may not be the best solution but it has worked many times for me. Try it sometime it might just make your life easier when you get challenged with a difficult piece.