Just for curiosity, I clicked on "Run Time Information" in My PhPAdmin and saw some of the stats listed in red (which I assume means not good)? Keep in mind that Threads is not the only Database running on my site. The items that show is red are specifically:
Slow_queries
537 - The number of queries that have taken more than long_query_time seconds.
Handler_read_rnd
2,582 k - The number of requests to read a row based on a fixed position.
Handler_read_rnd_next
338 M - The number of requests to read the next row in the data file. This is high if you are doing a lot of table scans. Generally this suggests that your tables are not properly indexed or that your queries are not written to take advantage of the indexes you have.
Qcache_lowmem_prunes
18 k The number of queries that have been removed from the cache to free up
memory for caching new queries. This information can help you tune the query cache size. The query cache uses a least recently used (LRU) strategy to decide which queries to remove from the cache.
Created_tmp_disk_tables
117 The number of temporary tables on disk created automatically by the server while executing statements. If Created_tmp_disk_tables is big, you may want to increase the tmp_table_size value to cause temporary tables to be
memory-based instead of disk-based.
Select_full_join
8,248 The number of joins that do not use indexes.
If this value is not 0, you should carefully check the indexes of your tables.
Sort_merge_passes
23 The number of merge passes the sort algorithm has had to do. If this value is large, you should consider increasing the value of the sort_buffer_size system variable.
Opened_tables
3,166 The number of tables that have been opened. If opened tables is big, your table cache value is probably too small.
Table_locks_waited
14 k The number of times that a table lock could not be acquired immediately and a wait was needed. If this is high, and you have performance problems, you should first optimize your queries, and then either split your table or tables or use replication.
Any of this suggest different setting in MySQL?