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How is memory usage on the box? If you are running out of memory, the CPU utilization may be driven by either swapping or OOM (out of memory killer) killing apps and them restarting. Might be wise to step up to the next larger instance size and monitor.
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I don't understand the way the AWS presents this information either, but I had very similar symptoms and in my case it DID turn out to be memory. I noticed that, out of the box, my Ubuntu instance had no swap space. I configured some (with swappiness=10) and it solved my problem. I did something close to what was recommended here:
answered 10 months ago
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I don't think this answers the question. There are maybe a number of things that could exhaust the CPU like what you mentioned that can result it reaching the burstable zone. However, as you can see on the screenshot I provided, my CPU burst capacity was still on almost 100% when it went to the burstable zone. I would expect that my server should still be operable until the burst capacity is depleted. For a feature that is there and you can see but doesn't do the job is false advertising in my opinion.