It sounds like what you really want is an INNER join. Drop the (+)'s and see if you get back what you're looking for. In addition, @GordonLinoff makes an excellent suggestion - get comfortable with using the ANSI join syntax, which is both more expressive and more comprehensible than the old-style "put all the conditions in the WHERE clause and then try to puzzle it out" style.
Here's how I'd rewrite this query using the ANSI-standard join syntax:
SELECT *
FROM PER_ALL_ASSIGNMENTS_F paaf
INNER JOIN PAY_ALL_PAYROLLS_F payr
ON payr.PAYROLL_ID = paaf.PAYROLL_ID
WHERE SYSDATE BETWEEN paaf.EFFECTIVE_START_DATE
AND paaf.EFFECTIVE_END_DATE AND
paaf.ASSIGNMENT_TYPE IN ('E', 'C') AND
paaf.PRIMARY_FLAG = 'Y' AND
payr.ATTRIBUTE1 = 'TINT' AND
paaf.EFFECTIVE_START_DATE BETWEEN NVL(payr.EFFECTIVE_START_DATE, TO_DATE('01/01/1000', 'DD/MM/YYYY'))
AND NVL(payr.EFFECTIVE_END_DATE, TO_DATE('31/12/4712', 'DD/MM/YYYY'))
One other minor matter. I notice you're using BETWEEN with date values which can potentially be problematic. Let's say, for instance, the you've got an EFFECTIVE_START_DATE of 01-JAN-2013 and an EFFECTIVE_END_DATE of 30-JUN-2013 on some row in PER_ALL_ASSIGNMENTS_F, and let's further say that the current date and time are 30-JUN-2013 at 07:02:04 AM. Given these data values, this row from PER_ALL_ASSIGNMENTS_F will NOT be selected, although you might expect it to be. The issue is that when the only fields filled in on a DATE value are the day, month, and year, then the hour, minutes, and seconds default to zero - thus the end date is really 30-JUN-2013 at 00:00:00, which is prior to the current date/time of 30-JUN-2013 at 07:02:04 AM, and consequently the date comparison causes the row to be ignored. I don't know how the EFFECTIVE_END_DATE fields are populated in your database - hopefully they're completely filled in, e.g. 30-JUN-2013 23:59:59 - but if not you might need to make your date comparison something like
TRUNC(SYSDATE) BETWEEN paaf.EFFECTIVE_START_DATE
AND paaf.EFFECTIVE_END_DATE
or
SYSDATE BETWEEN paaf.EFFECTIVE_START_DATE
AND paaf.EFFECTIVE_END_DATE + INTERVAL '1' DAY - INTERVAL '1' SECOND
(The former is probably a better choice, as the latter form will preclude the use of any non-function-based index which may exist on exist on (EFFECTIVE_START_DATE, EFFECTIVE_END_DATE).
Share and enjoy.