I have a PG dotRLN 4.6.3 site with 1500 class instances and the query "site-nodes" in acs-subsite/www/admin/index-postgresql.xql seems to be the problem.
Jeff and I have been looking at the query and talking on IRC. With 1500 classes I have 15181 nodes. The query does a permission check on every node so at 2ms per permission check that is 30 seconds.
We are working on a solution. Stop by IRC if you want.