The list of queries is ordered with the "worst" being first. "Worst" means that it has the most impact on the system, and probably should be the first to try to fix.
#1:
UPDATE phpbb_config
SET config_value = '1371551973'
WHERE config_name = 'rand_seed_last_update'\G
Please provide
SHOW TABLE STATUS FROM `db_name_adb` LIKE 'phpbb_config'\G
SHOW CREATE TABLE `db_name_adb`.`phpbb_config`\G
so we can dig into details as to why it averaged 5 seconds:
# Attribute total min max avg 95% stddev median
# ============ ======= ======= ======= ======= ======= ======= =======
# Exec time 53615s 200ms 430s 5s 14s 6s 5s
It is as if there is no index on config_name.
#2:
UPDATE phpbb_qa_confirm
SET question_id = 6,
attempts = attempts + 1
WHERE confirm_id = 'd53af5aa81074c0f5799250954730ac2'
AND session_id = 'e201dcff2ef8c8b3bf84f4e8749c3132'\G
needs a compound index on (confirm_id, session_id), in either order.
#3 looks truncated:
UPDATE phpbb_sessions SET session_time = 1371217872, session_page = 'ucp.php?mode=login', session_fo$
WHERE session_id = 'ce19e8d347a4eaf9$
Can you check?
It seems bad that so many of the seemingly efficient queries should take 10 seconds or more:
# 10s+ ###################
Is the server IO-bound? CPU-bound? Swapping?
Check the tuning:
http://mysql.rjweb.org/doc.php/memory
That may be the real issue!