1. That is odd! how are you evaluating the taxa returned?
2. 97% is the default similarity in both cases.
3. I'm not quite sure what you mean by 'NewOTU', but open reference OTU picking works by clustering the OTUs that don't initially hit to the reference database. So in other words, first you take out all the sequences you've seen before, and then the remaining sequences are compared against one another at the same similarity threshold. Does that make sense?