Simple queries take forever to run

I was going to post this on the performance page, but I assume its
something a novice gets stuck on.

This query: select count(*) from x where id not in (select id from y);
takes 1-3 seconds on sql server and runs forever on postgresql.

Both tables have an index on id
Table x has 1200673 rows
Table y has 1282 rows

shared_buffers = 64000
effective_chache_size = 400000

any ideas???