Hello Subodh,
is the Cisco switch used for inter vlan routing ( OSI Layer 3) or only as L2 device?
Is MTU set to 9000 on all L2 interfaces and all SVIs ( L3 Vlan interfaces)?
the issuemay arise because one host H1 can send a packet bigger then standard MTU to an host H2 that has only standard MTU. If all involved network devices support the bigger packet the frame is delivered to H2 where it is dropped
You should verify if an ICMP unreachable packet too big can travel back from H2 to H1 in order to make H1 aware of the reduced MTU of the other endpoint
see
http://www.cisco.com/en/US/tech/tk827/tk369/technologies_white_paper09186a00800d6979.shtml#t4
problems with Path MTU Discovery section
Hope to help
Giuseppe