MySQL missing databases

MySQL missing databases

I'm running MySQL 5.1 under Windows 7. If I start the MySQL Command Line
Client and type:
show databases;
it returns:
information_schema, aircraft_taxiing, dvd_collection, eqndb, mydb, mysql,
test and test_db
all of which are in the directory in my.ini:
datadir="C:/ProgramData/MySQL/MySQL Server 5.1/Data/"
If I open a command prompt window and type mysql it only gives
information_schema, test and test_db
What happened to the rest of the databases? I've been trying to connect
Python to MySQL using MySQLdb and can open any of the three databases, but
none of the missing ones. My goal is to make the Python connection in the
end, but I'd like to understand what's going on at the command prompt,
too.
Thanks.