Used countermeasures, but partially failed polygraph

[Grover]

I took a polygraph test recently and partially failed.

The countermeasures I used were controlled breathing and the pucker technique (which was not detected)

If I used the anal pucker and held my breath during control questions.

I breathed normal controlled breathing during relevant questions (any any question that was not a control question).

If my countermeasures were detected, I would have failed the entire test or been accused of using countermeasures.

Instead I passed one some questions and failed on others (all of which i was possibly lying)

I have to retake the polygraph and need to know some information.

If I was using normal breathing on the relevant questions, how is it possible that I was flagged as lying on some and not others?

I believe, but i am not certain, that the tester's computer made the determination of truthfulness and not the tester himself.

Could missing one control question throw off my results if i produced a reaction on all the other control questions?  Meaning if i failed to produce a reaction on one of the control questions, is it possible that a relevant question is paired with a specific control question to determine truthfulness so that failing to produce a response on the control question resulting in a lie on the relevant question? 

Any other theory why i might have failed on some relevant questions and not others even though I thought I maintained my breathing?