I'm getting random 404s as I change from various back-end plugins, pages, posts, settings, GET/POST events. I haven't used the front-end much yet to know if the problem is there as well, but this problem has been happening for weeks as I try and setup a new WordPress website.
I'm not sure if it's a server issue, php config or database corruption or just my incompetence, but I've just about ruled out every plugin/theme as just when I think I've eliminated the problem it comes back, so it seems random; sometimes things will work, other times not.
The sites are all on a shared server, but there don't seem to be any harsh limitations, such as resources, timeouts, max_mem and various limits.
If anyone has an idea what's happening with Akeeba in this extract of 404s from the access logs (taken over three hours only!), it may help me track down the issue: (and Akeeba did complete the backup to Amazon S3)
bingip [29/Nov/2015:19:11:37]"POST /wp-admin/admin-ajax.php HTTP/1.1" 404 13711 "http://mydomain.com/"
my.ip. [29/Nov/2015:20:14:53]"POST /wp-admin/admin-ajax.php HTTP/1.1" 404 24492 "http://mydomain.com/wp-admin/plugins.php"
my.ip. [29/Nov/2015:20:37:10] "GET /wp-admin/plugins.php HTTP/1.1" 404 25602 "http://mydomain.com/wp-admin/"
my.ip. [29/Nov/2015:20:43:30] "GET /wp-content/plugins/akeebabackupwp/app/backups/index.html HTTP/1.1" 404 25706 "http://mydomain.com/wp-admin/admin.php?page=akeebabackupwp%2Fakeebabackupwp.php&view=main"
my.ip. [29/Nov/2015:20:49:43] "GET /wp-content/plugins/akeebabackupwp/app/backups/index.html HTTP/1.1" 404 25696 "http://mydomain.com/wp-admin/admin.php?page=akeebabackupwp%2Fakeebabackupwp.php"
my.ip. [29/Nov/2015:20:50:29] "GET /wp-content/plugins/akeebabackupwp/app/backups/index.html HTTP/1.1" 404 25706 "http://mydomain.com/wp-admin/admin.php?page=akeebabackupwp%2Fakeebabackupwp.php&view=main"
my.ip. [29/Nov/2015:21:05:20]"POST /wp-admin/admin-ajax.php HTTP/1.1" 404 25691 "http://mydomain.com/wp-admin/admin.php?page=akeebabackupwp%2Fakeebabackupwp.php&view=backup&autostart=1&profileid=1"
my.ip. [29/Nov/2015:21:06:20]"POST /wp-admin/admin-ajax.php HTTP/1.1" 404 25691 "http://mydomain.com/wp-admin/admin.php?page=akeebabackupwp%2Fakeebabackupwp.php&view=backup&autostart=1&profileid=1"
my.ip. [29/Nov/2015:21:08:20]"POST /wp-admin/admin-ajax.php HTTP/1.1" 404 25691 "http://mydomain.com/wp-admin/admin.php?page=akeebabackupwp%2Fakeebabackupwp.php&view=backup&autostart=1&profileid=1"
my.ip. [29/Nov/2015:21:09:20]"POST /wp-admin/admin-ajax.php HTTP/1.1" 404 25691 "http://mydomain.com/wp-admin/admin.php?page=akeebabackupwp%2Fakeebabackupwp.php&view=backup&autostart=1&profileid=1"
my.ip. [29/Nov/2015:21:10:20]"POST /wp-admin/admin-ajax.php HTTP/1.1" 404 25691 "http://mydomain.com/wp-admin/admin.php?page=akeebabackupwp%2Fakeebabackupwp.php&view=backup&autostart=1&profileid=1"
my.ip. [29/Nov/2015:21:12:20]"POST /wp-admin/admin-ajax.php HTTP/1.1" 404 25691 "http://mydomain.com/wp-admin/admin.php?page=akeebabackupwp%2Fakeebabackupwp.php&view=backup&autostart=1&profileid=1"
my.ip. [29/Nov/2015:21:13:20]"POST /wp-admin/admin-ajax.php HTTP/1.1" 404 25691 "http://mydomain.com/wp-admin/admin.php?page=akeebabackupwp%2Fakeebabackupwp.php&view=backup&autostart=1&profileid=1"
my.ip. [29/Nov/2015:21:14:20]"POST /wp-admin/admin-ajax.php HTTP/1.1" 404 25691 "http://mydomain.com/wp-admin/admin.php?page=akeebabackupwp%2Fakeebabackupwp.php&view=backup&autostart=1&profileid=1"
my.ip. [29/Nov/2015:21:16:20]"POST /wp-admin/admin-ajax.php HTTP/1.1" 404 25691 "http://mydomain.com/wp-admin/admin.php?page=akeebabackupwp%2Fakeebabackupwp.php&view=backup&autostart=1&profileid=1"
my.ip. [29/Nov/2015:21:19:18] "GET /wp-admin/admin.php?page=akeebabackupwp/akeebabackupwp.php&view=configuration HTTP/1.1" 404 25728 "http://mydomain.com/wp-admin/admin.php?page=akeebabackupwp%2Fakeebabackupwp.php&view=main"
my.ip. [29/Nov/2015:21:19:26] "GET /wp-admin/admin.php?page=akeebabackupwp/akeebabackupwp.php&view=configuration HTTP/1.1" 404 25728 "http://mydomain.com/wp-admin/admin.php?page=akeebabackupwp%2Fakeebabackupwp.php&view=main"
my.ip. [29/Nov/2015:21:19:50] "GET /wp-admin/plugins.php HTTP/1.1" 404 - "http://mydomain.com/wp-admin/admin.php?page=akeebabackupwp%2Fakeebabackupwp.php&view=configuration"
my.ip. [29/Nov/2015:21:20:16] "GET /wp-admin/admin.php?page=toplevel_page_itsec_backups HTTP/1.1" 404 25657 "http://mydomain.com/wp-admin/admin.php?page=itsec"
my.ip. [29/Nov/2015:21:21:58]"POST /wp-admin/admin-ajax.php HTTP/1.1" 404 25648 "http://mydomain.com/wp-admin/admin.php?page=toplevel_page_itsec_settings"
my.ip. [29/Nov/2015:21:22:58]"POST /wp-admin/admin-ajax.php HTTP/1.1" 404 25648 "http://mydomain.com/wp-admin/admin.php?page=toplevel_page_itsec_settings"
my.ip. [29/Nov/2015:21:35:26]"POST /wp-admin/plugins.php HTTP/1.1" 404 25613 "http://mydomain.com/wp-admin/plugins.php"
my.ip. [29/Nov/2015:21:48:12]"POST /wp-admin/admin-ajax.php HTTP/1.1" 404 25644 "http://mydomain.com/wp-admin/plugins.php?plugin_status=all&paged=1&s"
my.ip. [29/Nov/2015:21:49:12]"POST /wp-admin/admin-ajax.php HTTP/1.1" 404 25644 "http://mydomain.com/wp-admin/plugins.php?plugin_status=all&paged=1&s"
my.ip. [29/Nov/2015:21:51:12]"POST /wp-admin/admin-ajax.php HTTP/1.1" 404 25644 "http://mydomain.com/wp-admin/plugins.php?plugin_status=all&paged=1&s"
my.ip. [29/Nov/2015:21:52:12]"POST /wp-admin/admin-ajax.php HTTP/1.1" 404 25644 "http://mydomain.com/wp-admin/plugins.php?plugin_status=all&paged=1&s"
my.ip. [29/Nov/2015:21:53:12]"POST /wp-admin/admin-ajax.php HTTP/1.1" 404 25644 "http://mydomain.com/wp-admin/plugins.php?plugin_status=all&paged=1&s"
my.ip. [29/Nov/2015:21:55:12]"POST /wp-admin/admin-ajax.php HTTP/1.1" 404 25644 "http://mydomain.com/wp-admin/plugins.php?plugin_status=all&paged=1&s"
my.ip. [29/Nov/2015:21:56:12]"POST /wp-admin/admin-ajax.php HTTP/1.1" 404 25644 "http://mydomain.com/wp-admin/plugins.php?plugin_status=all&paged=1&s"
my.ip. [29/Nov/2015:21:57:23] "GET /wp-admin/users.php HTTP/1.1" 404 25611 "http://mydomain.com/wp-admin/plugins.php"
my.ip. [29/Nov/2015:22:02:03] "GET /wp-admin/admin.php?page=toplevel_page_itsec_advanced HTTP/1.1" 404 25681 "http://mydomain.com/wp-admin/admin.php?page=toplevel_page_itsec_settings"
my.ip. [29/Nov/2015:22:03:29] "GET /wp-admin/users.php HTTP/1.1" 404 25643 "http://mydomain.com/wp-admin/admin.php?page=toplevel_page_itsec_advanced"