JK,
Certainly, something is taking extra time during some of your executions of the test. This is a valid result of your testing, and this is something you may want to search for to understand or to eliminate.
If you can disable interrupts during the encode() execution, do so. This may be difficult if some are being used. If needed, mask out the ones that are not required for the encode() execution. If one or more are required for execution, they should only be occurring as part of the encode() function execution; if they are sometimes inside the benchmark region and sometimes outside, this would explain big disparities in the measurements.
Benchmark sections of the encode() execution. You may be able to narrow down which portion has the variation and then track down what is causing it.
Regards,
RandyP