Polygraph "testing" has no scientific basis to begin with, and it's impossible predict what effect your anxiety will have on any given examination. However, even without an anxiety disorder, if one is more anxious when answering the relevant questions than when answering the so-called "control" questions, then one is likely to fail, regardless of whether one is telling the truth.

And polygraph chart readings aside, if you appear anxious to your polygrapher, this may be taken as a sign of deception and increase your risk of failing.

I think it would be prudent to read up on polygraph procedure and how to reduce the risk of a false positive outcome. See, for example, The Lie Behind the Lie Detector, especially chapters 3 & 4.