You need to group by just the date portion of CHECKTIME - try this or similar

SELECT inf.SSN AS EmpNo, Format(ck.CHECKTIME, "dd/mm/yyyy") AS CHKDATE,Min(ck.CHECKTIME) AS TIMEIN, Max(ck.CHECKTIME) AS TIMEOUT

FROM CHECKINOUT ck INNER JOIN USERINFO inf ON ck.Badgenumber = inf.Badgenumber

WHERE (((ck.CHECKTIME)>=#20/03/2013#)

Group By inf.SSN, format(ck.CHECKTIME, "yyyymmdd")

ORDER BY inf.SSN, format(ck.CHECKTIME, "yyyymmdd")