Upgraded to 5.3 and updated all the modules so started the integrity check and this appeared in the log files :-
Array
(
[error] => Query Error: You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near '' at line 1
[_post] => Array
(
[_uri] => /core/integrity_check_save/__ajax=1
[jr_html_form_token] => bf585d54fdc45f892749c1be19cd7958
[jr_html_form_profile_id] => 1
[jr_html_modal_token] => 24d2a456d6f37536e8cf197e7c13d037
[validate_modules] => on
[validate_skins] => on
[repair_modules] => on
[repair_tables] => off
[optimize_tables] => off
[module_url] => core
[module] => jrCore
[option] => integrity_check_save
[__ajax] => 1
)
[query] => UPDATE jr_jrgroup_member SET member_active = '0' WHERE `member_user_id` =
)
Check has been stuck on the users module for over an hour now (16,000 users).
MySql version is 5.6.28-76.1
Cheers
updated by @white-agency: 05/27/16 09:28:00PM