If the counters are going up i believe that the frames are being dropped, could be due to FCS error also. If you are having trouble configuring Jumbo Frames, i can provide some info that maybe useful.
Firstly Cat 6500 supports Jumbo Frames up to 9216 bytes but some line cards support Jumbo Frames only up to 8096 bytes due to some ASIC limitations. You can try and decrease the Frame size to 8096 on cat 6500 and a bit lower on the Server.
Secondly you have the following commands for configuring MTU and Jumbo Frames
(config)#System MTU 1500
(this applies to all interfaces)
but if you configure the following command
(config)#System MTU jumbo 9000
(this only applies to Gig ports and 10/100 ports use the system MTU setting)
also note that if you have configured Jumbo Frames that ingress on a Gig ports and egress on a 10/100 port those are dropped.
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