Hmmm...the updated plan is estimated to run FASTER than before, but the actual execution time is horrible.
Is this on the same machine, Nima? Both plans look good. I don't see why they would be different because the CVS LOG shows no changes to the query. Can you do a hand-inspection of the query on your 2.0.6 instance and your 2.1 instance to see if there's actually a difference?
My guess is that it's going to disk in the second case. Can you use TIME (put the query in a file and do a "time psql dbname -f the_file_with_the_query) to see how much CPU time vs. disk time is being used in this query?
My comments above still stand at least in regard to the acs_perm call in the WHERE clause ...