You can only have ONE "hold" node with synchronize option enabled in your whole workflow.
As said, in 1.0 (and the betas) the problem is already sorted out.
I think to workaround your current problem, it should be easy for you to get rid of 2 unneccessary hold nodes (with sync option enabled) that are in your workflow before all the encodes are done. Replace them by either Hold nodest that are set to sleep(1) or by some populate variables or delete them completely
