I still have to investigate on this but it seems when you enable library override on a material, the material slot doesn't sync on the slave computers, causing the sync to fail.
I'll give a simple example when I have the time.
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Woops! I was using relative paths for a library that was sitting in my common server. Using absolute paths solved the issue. Maybe it would be a good thing to have some sort of warning for that in the log, such as adding this line at the end:
Sync failed: Are you using relative paths for a remote library? If so, try changing it to an absolute path".