Thanks for sharing your experience with us.
I am a still a little bit unclear about what exactly it was that you were doing that seemed so unusual to the proctors. It sounds like you went through on the computer (before looking at slides at all) and very quickly just clicked an answer for every single question (like maybe "A" for everything?). Then you wrote all of your answers down as you went through the slides in order, then put them all into the computer at the end. Is that correct? Although I don't know that I, personally, would use a technique like that (I would probably just put each answer in as I looked at each slide because I would be worried about running out of time to input all those answers at the end), it doesn't seem all that odd to me. Also, on the second (CP) day, was the proctor asking you about your technique from the AP slide session the day prior or about something you were doing at that moment during CP session itself? Either way, it seems completely inappropriate for them to interrupt you and waste your time during the actual testing session itself (not to mention interrupting the other test-takers) for something that was not in any way against "the rules."
I know in previous years I heard rumors (here on sdn and other places) that some test-takers would deliberately put slides back into the slide boxes out of order and in a disorganized fashion to sabotage the next person who got that box. Perhaps they are cracking down on this and that is why there was so much concern about how you were handling your slides?