netflow analyzer performance too bad

For twenty testing of the netflow analyzer. The result as follow:
1. Hardware.
IBM 365X PC server 2XCPU(Xeron)
4GB Memory
7200 RPM Harddisk (160GB)

2. NetFlow Package number is about 5M/day.
For current one hour query:
Traffic - 5 seconds
Application - 6 seconds
Source - 4 mins
Target - 5 mins
Conversation - 7mins
3. We have tunning some parameter for java and mysql db as follow:

$DB_HOME/bin/mysqld --no-defaults $useropt --basedir=$DB_HOME --tmpdir=$TMP_HOME --port=$DB_PORT --socket=$TMP_HOME/mysql.sock --default-table-type=INNODB --set-variable=query-cache-type=2 --read_buffer_size=1000000 --read_rnd_buffer_size=520000 --sort_buffer_size=4200000 --myisam_sort_buffer_size=16000000 --key_buffer_size=96000000 --innodb_buffer_pool_size=156000000 --bulk_insert_buffer_size=16000000 --table_cache=128 --low-priority-updates

$JAVA_OPTS -Xms256m -Xmx2048m

Please why we use so good performance's hardware and get so bad netflow analyzer performance.

Thanks.