I got this error message and thought I would post my solution here in case it helps someone else.
It turns out that I had this problem, even when using an account I had configured as sysadmin on the server. For example, I could connect to the SQL server with SQL Server Management Studio with this account and could see the database and all the tables. However, when I connected with the same account in DB Connect\SQL Explorer, it would show all of the databases in the Catalog combo box, but I would get an error message for the Schema combo box, "Cannot get schemas."
I turned on DB Connect logging and would see the following error in the log file:
ERROR c.s.d.s.a.s.d.impl.DatabaseMetadataServiceImpl - Unable to get schemas metadata
com.microsoft.sqlserver.jdbc.SQLServerException: Invalid object name '[my_database].sys.schemas'.
I turned out that this problem was because I was using the MS SQL Server JDBC driver version 7. When setting it up, I figured I would ignore Splunk's guidance to use version 4.1 or 4.2 and use the latest available version. Turns out this was a bad idea.
In my testing if I copy the version 4.2 driver into the folder and restart, everything works great. Then if I copy the version 7 driver into the folder and restart, I get this error message (without any changes to permissions or anything).
Anyway, hope this helps someone.
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