To address your questions, respectively:

1. It's unlikely that the polygraph operator had any confidence that you were using countermeasures. Were that the case, you would likely have been accused of "manipulating your physiology" and badgered for an admission.

2. Yes.

3. Yes.

thanks for your reply, George

i have a couple questions:

-if the poly examiner thought i was using countermeasures, why did they invite me back for another poly?

-do i have a lower chance of get a clearance that doesnt require a poly?

-if I apply for a clearance that doesnt require a poly, will the adjudicator check the scattered castles database?

Yes and yes. Details of your polygraph experience will have been entered into an inter-agency federal database called Scattered Castles.

thanks for your reply

if i apply for a job with another agency that doesnt use the poly, will they know that i didnt pass the poly for the other govt agency? will failing previous poly make it harder for me to get an interim security clearance and a final clearance for another govt agency?

Yes, the technique of requiring the examinee to repeat the last word of the question is a counter-countermeasure. It's an attempt to prevent the examinee from engaging in mental dissociation, or thinking about something other than the question being asked.

I can't venture a guess as to your chances of getting a clearance with the present government agency or any other. But if the agency involved was either the CIA or NSA, which use the relevant/irrelevant technique, you should know that it is not uncommon for applicants -- even those eventually hired -- to initially be told that they are having problems clearing the test, to be pressed for admissions, and to  be invited back for one or two "re-tests."

during my poly, examiner had me repeat the last word of her question followed with my answer.

questions:

-was this a counter-counter measure?

-i was invited back for another poly. what are my chances of getting a security clearance with another govt agency now?