Upvote:1
The OP updated the information in the question. There was a note on the file because they were using two different passports and that was the reason the ESTA was rejected.
They got a visa without problems, as traveling with two different passports is allowed.
What we can learn from this is that if you have two different nationalities and so far only used one to travel to the USA, it might be best to stick to using that nationality so you avoid the note and possibly future problems.
On the other hand, if you get a new nationality which can get you an ESTA or a visa with easier, it might be worth it to use that passport. You can clear up the confusion by contacting the consulate and applying for a tourist visa, or maybe even already get the note on your file taken off by just explaining and asking for it.