If you have the output of show process cpu sorted at the tine of the issue, also check if there was any IGP flapping or STP topology changes that might caused the high CPUSent from Cisco Technical Support iPhone App
You are absolutely right, the counters are only incrementing if the packets hit the gateway, but when these packets moving from one access port to another within the same vlan they will not hit the gateway so it will not be countedSent from Cisco Tec...
Are these switches directly connected or there are some switches or L2 cloud between them? This issue is seen when there are other devices in the middleSent from Cisco Technical Support iPhone App