9304 High CPU usage, packet loss.

[Heathkit]

Hi!
We have a 9304 which is experiencing intermittent high CPU usage and packet loss. The CPU/IP process runs up to 100% for a while. At the same time we experience packet loss/high roundtrip time. Then everything is back to normal. Users that run Citrix/Terminal sessions and VPN tunnels loose their connections or experience then cery sluggish.
We run the latest SW.
We run trunks, BGP routing, ACL-list and more.
What should I do to troubleshoot this? Help wanted!
I have tried to remove one of the trunk cables and then the CPU and everything went back to normal, for some hours. If I do a sh span I see that Spanning-tree is not configurerd to any port-vlan, but when I do a sh int I can see that STP is configured to ON. What does that mean?
The 9304 is connected to another 9304 and to 5300 with trunks. One of the 5300 is a member in a mesh.

[Tijl van der Steeg]

Sounds like a STP problem indeed.
Could you please post the config and the output of show span?