Spot on stair tread won’t take stain

[GRofVA]

I stripped, sanded and refinished my stairs in my house which is almost 40 years old.   The stair treads appear to be made of pine and were once covered in carpet prior to us purchasing the home in 2011.   Obviously there are a lot of imperfections and carpet staple holes so I’m not looking for perfection.   I purchased American Tecnologies “WoodFil EPOXY” wood filler for some rather large spots of which one was right on the rounded front edge of one of the treads.  Everywhere else I used it, the filler and surrounding wood accepted the stain just fine so I’m not convinced the filler is the issue.  This one spot on the top tread (of course) where I filled in a large indentation with the filler and it’s surrounding area will not darken up.  I used General Finishes “Java Gel” oil based stain.  I tried “roughing up” the area with coarse sandpaper and that didn’t work.  I tried applying mineral spirits to “open up the grain” and left the gel stain on for an extended period and that didn’t work either.  I have searched the web and YouTube under multiple search criteria and cannot find a solution to this issue.  Willing to try any suggestions? 

[gee-dub]

No one else has taken a poke at this so I will give it a shot.  Obviously something has gotten into the fibers that is resisting the colorant.  This may be one of those situations where the effort required to figure it out out weighs the benefit of knowing.  In finishing it is all about surface prep.  Irregular surface or material results in the finish reacting differently.

Even if you were to sand that entire tread down 1/32" and reapply, you will get a different result, only now it is the whole tread.  I'll assume your ultimate finish will be a clear floor finish of some sort.  I would try to get a dye or mix a dye with a gel stain to get a color match and literally "paint" the offending area.  You may need to add bits and strokes of other colors to get a good overall match with the surrounding area.  You will then rely on your top coat for protection.