Can you tell me some more context of what version and OS you are using? I am unable to replicate this using Windows 10, After Effects CC 2018 (15.0.0), Media Encoder CC (12.0).
Are you able to create any other compositions that do the same thing? Such as a very minimal composition where this seems to happen. Also have you tried clearing your media disc cache in After Effects? It is possible that the cache coherency between After Effects and Media Encoder has gotten compromised.