I've been fiddling around with a Fire TV Cube (3rd) to tackle the exact same issue. Both TrueHD and DTS-HD playback fine, but E-AC3 with Atmos metadata stutters like hell. I also have a Shield TV Pro (2019) running KODI 19.5 and as far as I know it doesn't have that issue, but I'll double check it tomorrow.
It's a few weeks later (I forgot about this post) and I can confirm that the E-AC3 issue is isolated to the Fire TV Cube (3rd). When using KODI Nexus RC2 on the Cube, I'm unable to passthrough E-AC3. There's just no audio. Every other audio format (i.e. AC3, DTS, TrueHD, DTS-HD MA) will playback flawlessly. Has anyone else experienced this on the Cube as well?