I have reported that problem to the authors of eac3to and DcaDec (
here and
here) but currently there is no good solution. As you can see, the error happens only when the DcaDec is configured with the "strict decoding" option turned on. Unfortunately, the author of DcaDec doesn't want to fix the problem, and the author of eac3to doesn't want to remove the "strict flag", so currently we're stuck. I have requested an option to turn the strict flag off with the command line of eac3to, but it will be implemented only in the next version of eac3to.
I have therefore implemented a workaround in the latest version of BD3D2MK3D (v0.77): When the DcaDec DTS decoder fails with the synchronisation error, the conversion is restarted with the Libav decoder. Libav works but it is less good (because it decodes only the lossy DTS core), so I've kept DcaDec by default. I have also been able to verify that a lot of DTS HD or MA tracks can be decoded correctly by DcaDec with the strict flag (but I agree that the problems are frequent too). AFAIK, the Libav workaround works when it should, but I've implemented it ONLY when the error reported by DcaDec is the synchronisation error. If you encounter often another error and the conversion is not restarted automatically, please post here the part of the log with the error message. I may have to trap other errors as well.
Note that the workaround is not automatic when you convert manually the DTSHD/MA track with Convert Audio from the Tools menu. In that case, if the error happens, you have to manually select the Libav option and restart the conversion.