The physical port is set to 1500 but the MTU administrative of the port is 9000.
When the NIS server is set to 9000 MTU, MSS (Maximum Segment Size) negotiated is 8960. This is when NetApp is dropping the packets causing incomplete group information about the user leading to access denied.
NIS server showing only primary group information:
cluster::*> getxxbyyy getgrlist -vserver svm01 -node Node01 -username user1
(vserver services name-service getxxbyyy getgrlist)