confused,
Your polygrapher lied to you when he told you he was collecting a chart "to see if you could respond to the polygraph." The purpose of this procedure, formally known as the "acquaintance test," but commonly referred to as the "stim (short for "stimulation") test," is to dupe the examinee into thinking that the polygraph can actually detect deception.
Everyone is told that they reacted strongly to the number they chose, whether or not they did. It is not uncommon for polygraphers to show the examinee the chart in cases where the examinee really does react strongly to the number chosen.
It is also not uncommon for polygraphers to show polygraph charts to examinees and point to supposed reactions and demand an explanation. However, your account is the first I have heard of a polygrapher showing a subject a chart with only one tracing. The standard polygraph chart includes four tracings: upper and lower pneumo, electodermal, and cardio. Polygraphs with a motion sensor (used in an attempt to detect countermeasures) may have a fifth tracing for that.
It's possible that the polygraph software enables the operator to print out a single tracing rather than all of them. It's also possible that the printouts you were shown (both from the "stim test" and later, during the "in-test" phase) were not actually your own, but pre-planned props. I don't know.
For more on polygraph procedure, see Chapter 3 of
The Lie Behind the Lie Detector. In any event, you'll be glad to know that the Department of Defense's counterintelligence-scope polygraph screening program has a pass rate of close to 100%. Although some individuals may be initially accused of deception and scheduled for a "re-test," virtually the only persons who ultimately fail are those who make "substantive admissions."