My guess is that this is the problem

Hash Cond: ((table1.id)::double precision = table2.id)

Your query is casting the table1.id to something with a fractional portion. This likely throws off planner estimates. Is id an int or a double? Try removing your cast.

Also, don't write SQL-89:

SELECT id
FROM table1
INNER JOIN table2 USING (id)
WHERE ST_Intersects(
  ST_Transform(ST_SetSRID(table2.the_geom, 2768), 4326), 
  ST_SetSRID(
    ST_MakeBox2D(
      ST_Point(-122.2119140625,38.013476231041935), 
      ST_Point(-122.18994140625,38.03078569382294)
    ),
    4326
  )
);