trouble with SQL bindings

Your issue isn't exactly with query bindings or CI, you'd have the same issues if you ran the queries directly on the DB. Maybe try this..

PHP Code:

SELECT srat.employee_email, srat.taxyear, sr.item, kt.qualified, kt.unqualified
FROM survey_results_activities_temp AS srat
LEFT OUTER JOIN survey_results AS sr ON sr.user_email = srat.employee_email AND sr.taxyear = srat.taxyear
LEFT OUTER JOIN key_temp AS kt ON kt.activity = sr.item
WHERE srat.employee_email = ? AND srat.taxyear = ?
GROUP BY srat.employee_email