MySQL Handler_read_rnd_next == tablescans without indexes?
You should enable slow-query-log and log-queries-not-using-indexes to in order to manifest what queries are skipping on the indexes.

This is just a personal preference, but I usually the --processlist option of mk-query-digest. I wrote a automation script for it long ago : MySQL general query log performance effects based on Percona's video about mk-query-digest being a replacement for  the slow log.

Once the queries are made known, you will have run EXPLAIN on all selects. Any query whose EXPLAIN plan fails to choose an index is guilty of doing the table scans.