Video stutter after render in Media Encoder

Original file is a 12 min. 4K 30fps iPhone video that plays back without any problems.

After editing down to under 6 min. and doing some color correction in AE, every attempt at rendering in Media Encoder, no matter what codec I choose (including ProRes 4444), always results in certain sections of the video playing back stuttering at a reduced frame rate.   Those sections are always the same in each instance.  I also tried reducing the resolution in ME to HD and get the same stuttered result.