When using sqlite3.Row as the row_factory for a sqlite3 connection and 
performing a SQL join that returns rows from two or more tables with 
identical column names, the returned sqlite3.Row object contains 
duplicate keys.  Subsequently, when trying to access values by key, only 
the value contained in the lowest numbered index matching the key is 
returned.  Additionally, attempting to use the keys returned to create a 
new table in the database fails due to a duplicate column name error.

A better behavior would be for the sqlite3.Row object's indices to be 
prefixed with table names for cases in which a query produces results 
from two or more tables.

I think this is a sqlite issue, not a Python one.
cursor.description should return unique column names.

See http://www.sqlite.org/cvstrac/tktview?tn=3221

Try upgrading to the latest sqlite release. Or set "pragma 
full_column_names=ON;"

import sqlite3
conn = sqlite3.connect(':memory:')
cursor = conn.cursor()
cursor.execute("create table T (a, b, c)")
cursor.execute("insert into T values (1, 2, 3)")
cursor.execute("insert into T values (2, 3, 4)")
conn.commit()
cursor.execute("pragma short_column_names=OFF;")
cursor.execute("pragma full_column_names=ON;")
cursor.execute("select * from T T1, T T2 where T1.a=T2.b")
print [d[0] for d in cursor.description]
# output: ['T1.a', 'T1.b', 'T1.c', 'T2.a', 'T2.b', 'T2.c']

Ah, that's it.  Thanks for the tip, this issue can be closed now.