This will happen if servers are different versions and if one is from before and the other after a specific point in time.  The 'specific point in time' is late summer/early autumn 2008.

Versions released before before this time had a bug with the SHOW FULL FIELDS command.  SHOW FULL FIELDS is used by Data Sync to verify that the <source> and <target> schemas for a table are identical.  The server bug is that SHOW FULL FIELDS returns NULL for the DEFAULT of a string column even if it is declared DEFAULT '' (empty string).

So you may even have noticed that SHOW CREATE TABLE will return the same for a table of the two servers involved and still Data Sync refuses to perform sync telling that schemas are not identical! But is is not SHOW CREATE TABLE but SHOW FULL FIELDS that matters in this context. And that is the explanation!

The same server bug affects Schema Sync.  This is described here.