Without any changes on either client or server, I was getting this error when running SQL Compare 8.1:
Registering data sources - reading tables
An entry with the same key already exists.
The Profiler indicates that the last SQL issued by SQL Compare is as follows:
d.is_fulltext_enabled AS FullTextEnabled,
d.is_encrypted AS IsEncrypted,
dec.key_algorithm AS KeyAlgorithm,
dec.key_length AS KeyLength
FROM sys.databases d
LEFT JOIN sys.dm_database_encryption_keys dec ON dec.database_id = d.database_id
WHERE d.database_id = DB_ID()
I happen to have a copy of my target which is one moth old. I was able to successfully run SQL compare against that old copy.
I upgraded to the latest version, 10.4.8.87 - that did not fix the problem.