I don't know if you've done this, but it's always a good idea to rent two sanders for floors. The big drum one plus the smaller circular sander with the two handles on the top of it.
I think OG is right when he said that some areas must have a lot of deeply embedded grease or varnish. That would explain the bits where the stain didn't take.
Wood dyes need a well sanded uniform surface to take evenly. To be honest, with an old floor, I wouldn't even attempt it. There are plenty of floor sealers around, but all the ones I've ever seen are clear, not coloured. "Junckers Strong" and "Dulux Diamond" are my favourites.
I'm sorry you have had such a disaster. It's going to take a lot of sanding to accept a dye successfully. Perhaps you could look at using a coloured varnish stain. A finish with the colour actually included in the varnish will be more successful.