I think I know what the issue is, but I lost my hard drive on my development machine so I am currently down.
Did you currently have the source code installed?
If so, if you open up ScriptDatabase.cs (under SQLAzureMWUtils project) and search for SQLHelper then comment out this section:
string connectionStr = "server=" + _ServerInstance + ";database=" + _sourceDB.Name + ";uid=" + _Login + ";pwd=" + _Password;
using (SqlConnection con = new SqlConnection(connectionStr))
ScalarResults sr = SqlHelper.ExecuteScalar(con, CommandType.Text, "SELECT COUNT(*) FROM [" + tbl.Owner + "].[" + tbl.Name +"]");
if ((int) sr.ExecuteScalarReturnValue < 1) return;
You will probably be good to go.
If you are not setup for this, then as soon as I get my developer machine rebuilt, I will fix and upload a new version (3.5.6).
Sorry about this,