Most likely you did nothing wrong...but your assumption is most likely wrong.
The rebuilder rebuilds everything which passes a checksum check. It takes a file, calculates the crc32, looks in the currently used datfile and recreates all matched instances in the destination using the found filename.
"Header support" only means that for the checksum calculation it takes special rules into account. In the NES file the rule is like "If the file starts with the NES token, skip it and calculate the checksum for the rest of the bytes only".
So...it depends what the datfile holds...enabled NES header support does not necessarily mean you only rebuild files with NES headers.
So maybe it helps if we pick one file out of your collection. What's the file's crc32 (full file), does this checksum appear in the datfile.......Does the file start with NES token, what's its checksum without it? Does this crc32 appear in the datfile....
so...such things need to be double checked.