Permalinks plugin not creating links for existing records

Hi

I am struggling to make the 'Update Tables' function work on the permalink plugin. I have run the debug and this is the results. Lots of 'non-existent-url' references, which i assume isn't right:

$server[] = array (
'date' => '2018-01-23 15:17:06',
'HTTP_HOST' => 'my domain name here',
'SERVER_SOFTWARE' => 'Apache',
'PHP_VERSION' => '5.6.33',
'PHP_UNAME' => 'Linux [info removed] #1 SMP Wed Jan 17 13:19:23 EST 2018 x86_64',

'_NOTES_' => '',
'---------' => '---------',
'CMSB_MOD_SECURITY2' => '1',
PHP_SELF' => '/cmsb/plugins/permalinks/permalinks_dispatcher.php',
'PHP_SELF_ORIGINAL' => '/cmsb/plugins/permalinks/permalinks_dispatcher.php',
'QUERY_STRING' => 'this=that',
'REDIRECT_QUERY_STRING' => 'this=that',
'REDIRECT_SCRIPT_URI' => 'http://mydomainname/non-existant-url',
'REDIRECT_SCRIPT_URL' => '/non-existant-url',
'REDIRECT_STATUS' => '200',
'REDIRECT_UNIQUE_ID' => 'WmdR8sCQUOwDwCbCCHY4RwAAAAE',
'REDIRECT_URL' => '/non-existant-url',
'REQUEST_URI' => '/non-existant-url?this=that',
'SCRIPT_FILENAME' => '/home/xxxx/public_html/xxxx/cmsb/plugins/permalinks/permalinks_dispatcher.php',
'SCRIPT_NAME' => '/cmsb/plugins/permalinks/permalinks_dispatcher.php',
'SCRIPT_URI' => 'http://mydomainame/non-existant-url',
'SCRIPT_URL' => '/non-existant-url',
--------' => '--------',
'_OUTPUT_ACTUAL_' => '/non-existant-url',
'_OUTPUT_EXPECTED_' => '/non-existant-url',
);

Thanks