Hello Eungyeong lee,
It uses different paths through the associations(see bold):
1)
[UserManager.Employee_Department
/UserManager.Department
/UserManager.Employee_Department_Security
/UserManager.Employee
/UserManager.Employee_Account='[%CurrentUser%]']
2)
[UserManager.Employee_Department_Security
/UserManager.Department
/UserManager.Employee_Department
/UserManager.Employee
/UserManager.Employee_Account='[%CurrentUser%]']
This can hold different results because you retrieve over different paths also this can hold different performance depending on the amount of records that needs to be searched through.
Hope this helps,
Good luck!