I tried staining the treads on some stairs we had installed. And, for the most part, it looks really good. But, the stain didn't seem to take in a couple areas. Here is an image showing one example where the stain didn't take

For background, here was my procedure:
- Sanding
- Apply mineral spirits, wait for drying
- Apply pre-stain
- Apply stain, and wipe off excess stain
My guess was that there was some contamination in the area that didn't take stain and that I simply hadn't sanded enough through this. So, I sanded just that area and applied the stain again. But, this didn't seem to help much. Here is how it looks now

So, I have a couple questions, with the main one being: What should I do?
Some other thoughts/questions I have:
- Is the problem with my "fix" that I should have also applied a pre stain again? Because, in the second picture it does seem like some of the stain took, but it clearly doesn't match with the original. So, maybe it's because I didn't use pre stain?
- I clearly increased the "bad" area in size a bit with my sanding. I find it interesting that this new area all looks consistent with itself now (but not with the rest of the wood that originally took stain). I think this is perhaps consistent with the idea that I needed to apply the pre stain to this bad area to make it look consistent with the "good" parts?
- In the second picture, the "good" part of the wood that has taken the stain looks a bit different from the first picture. Not sure if it's the lighting? Or does the stain change over a couple days?
- Is it bad that I haven't applied polyurethane to the good areas yet? I was wanting to wait until the bad area looks good.
Thank you for any help!