I am finishing 1,000 sq ft of white oak flooring using Varathane oil-base floor finish. Half the flooring is new, the other half is 40 years old. In one of the 5 rooms I am finishing, I have experienced a problem where I get a sort of pronounced raise of the grain with each coat of finish I apply. It only occurs in this room, and does not occur to a section of new boards I installed in this room to patch a pet stained area. I have applied three coats so far, and have sanded between each coat. However, with each coat the problem seems to get worse, and not better. The defect in the finish is sort of a minor alligatoring that corresponds to the grain pattern of the wood itself. I do not know if it is grain raise, or if it is some kind of contamination in the original flooring that was not removed by sanding. Any ideas on how I might deal with it? As I had said, this is not happening on the other 800 sq ft I am finishing, but is just in this one room.

It does sound like contamination in the old flooring. Something got into the wood and is interfering with the finish. I'm afraid the only recourse is to remove the offending boards and resand that room.