Can you export another flavor of quicktime from Toonboom and RVIO? If so, can you try exporting to Quicktime Animation and see if the problem still occurs?
The files imported are h264 encoded .mov files.
That's not the best format to be working with. You should export something like Cineform or DNx from your animation software for continued editing. Don't ever go down to H.264 until final delivery.
As commented on in the post, we tried swapping to proresLT, which solved the "problem".
We only use h264 as a proxy format for the editing process, we do final conform and delivery using EXRs and Nuke Studio.
We are currently rebuilding the projectfiles using XML to see if this helps. Ive written a script to sort video and audio-layers into bins. If the problem reoccurs after rebuilding the projectfiles, we might consider moving to a different proxy-codec.
We only use h264 as a proxy format
That's a poor choice for proxy. H.264 is much more difficult to edit than Cineform, DNx or ProRes.
We will consider swapping out our proxy-format, but this does not necessarily address the bug in question, just circumvent it.
And it will seriously take time and effort on our pipeline and crew to convert input files and project files. (We are talking a number of quicktimes in the 5 digit-range.) Swapping to prores or similar will also take a bigger toll on our file server and network speeds because of the increased file sizes.
I thought Premiere should work well, regardless of input format. Unlike other editing suites which prefer transcoding to a specific intermediate codec beforehand?
We will try taking the route through XML and back, but need to be vigilant on the effects not carried over in the xml-file. The xml-translation-logfiles should help with this.
this does not necessarily address the bug in question, just circumvent it.
Sometimes, that's all you get.