As advised we are testing the following workaround listed here:
http://social.msdn.microsoft.com/Forums/en-US/ssdsgetstarted/thread/7194e74f-ee1e-4116-af1c-6e991ebe6dfa
1) We create a temp database and create by script the tables we want to replicates on the database (less than 500 tables per synchronisation group)
2) We create our synchronisation group, with our source database as the main database, we add our temp table and our destination table
3) We select the tables we want to replicates from the temp table schema information
4) Finally we remove the temp table from the sync group
It seems to be working so far.