I would start by comparing the data in the two systems. Pick a table and compare the values between the two. It COULD be that the user expected data, but data didn't actually exist in the MySQL side, it could be that the data needs to be decrypted before it can be used, it could be that the end user is trying to do something unexpected with the data (decrypt, encrypt, convert, etc) and isn't getting the expected result.
So, my first step would be to log into each system and manually have a look at a row. Do a comparison on that individual row and make sure that to you they appear to match. THEN get a row from a user and compare it between the two systems to make sure they match. It could be something like the tool the user is using doesn't work properly with VARBINARY(MAX) and needs it in another datatype, or the tool doesn't work properly with SQL Server.