I am using comquest and going through it the second time around. I really like their questions and explanations. I saw those questions too but this is exactly what I love about this question bank. For example, the questions you mentioned - I realized they are asking the most likely cause of the condition is... and you have to choose from the best options given (sometimes not the best answer) but their explanations always go into details and explain it and give the best answer there or tell you how to approach this type of question. I commented on the question about the vomiting patient and realized the patient was vomiting because it was a reaction to some other drug and the question was asking what you should switch them to (2nd line agent), right?. I agreed with their response. And for the questions with more than 2 correct answer options, that is what my classmates have complained about with the actual COMLEX. I chose poliomyelitis on that question because it wasn't ascending paralysis. I'm pretty sure that was the right answer. I am feeling much better with these style of questions the second time around and taking the real thing in a month.
It's quite unfair that the NBOME doesn't state one reference source to use. To answer your other questions, I agree with the other poster that your knowledge is there given you went through FA 3 times and 80% of UW but it takes getting used to these questions and not just knowledge.