This is such a specialized question, at the intersection between neurology and cardiology, that I think it probably belongs in the 'Expert Forum' here:
Certainly, you'd get a more complete answer than you'd likely get from us here, though we are a reasonably well-informed group of patients.
That said, I'll venture that description of yourself--apart from the Chiari malformation--indicates that you are in a low-risk group for heart disease, being young, female, normal-weight, and basically healthy. However, your cardiologist will definitely ask about your family's heart history, which is often relevant.
It sounds as though you might be--very rarely--experiencing a very small number of sinus pauses interspersed with normal beats. 3 seconds is a bit 'out there,' and if you had more of them more often, you might even faint, but you don't mention experiencing that, and I'm sure you would have noticed it.
Your cardiologist will probably be checking out your heart to see if you have any purely heart conditions, unrelated to your Chiari, that could be causing your pauses, like dysfunction of your SinoAtrial Node (the heart's pacemaker), or various types and degrees of heart block, or certain kinds of rare congenital heart disease, or even if you've ever had a heart attack that might have caused some damage.
If you're really worried, try posting your question in the Expert Forum. But my advice to you would be, if you can, to just to write down your questions for the cardiologist before you see him, and otherwise not to fret too much. Your best source of information will be the doctor who actually has your heart and your history in view.