I see something similar, but not exactly:

ERROR: sql query: SELECT u.id FROM #__users u LEFT JOIN #__core_acl_aro a ON a.section_value = 'users' AND a.value = CAST( u.id AS CHAR ) WHERE a.value IS NULL : returned error: Illegal mix of collations (utf8_unicode_ci,IMPLICIT) and (utf8_general_ci,IMPLICIT) for operation '=' SQL=SELECT u.id FROM jos_users u LEFT JOIN jos_core_acl_aro a ON a.section_value = 'users' AND a.value = CAST( u.id AS CHAR ) WHERE a.value IS NULL

Notice, utf8_unicode_ci,IMPLICIT is the same for both tables, but still get the error when running CB Tools: Check Users database: Results

do what I found in this thread and see if you have other tables that are not using the same collation:
forums.devshed.com/mysql-help-4/change-all-collation-types-in-db-698907.html

Thanks. I ran that, but MySQL returned an empty result.

I reran the CB Tools: Check Users database with the same result.

[code:1]
Checking Users Datbase:

All Community Builder comprofiler table rows have links to user table.

All users table rows have links to comprofiler table.

users table has no zero id row.

comprofiler table has no zero id row.

All rows in comprofiler table have user_id columns identical to id columns.

ERROR: sql query: SELECT u.id FROM #__users u LEFT JOIN #__core_acl_aro a ON a.section_value = 'users' AND a.value = CAST( u.id AS CHAR ) WHERE a.value IS NULL : returned error: Illegal mix of collations (utf8_unicode_ci,IMPLICIT) and (utf8_general_ci,IMPLICIT) for operation '=' SQL=SELECT u.id FROM jos_users u LEFT JOIN jos_core_acl_aro a ON a.section_value = 'users' AND a.value = CAST( u.id AS CHAR ) WHERE a.value IS NULL

All ACL core_acl_aro table rows have corresponding entries in users table.

All core_acl_aro table rows have ACL entries in core_acl_groups_aro_map table.

All core_acl_aro table rows have ACL entries in core_acl_groups_aro_map table.
[/code:1]