Problem - configure connections to not pass BPDUs without disabling STP on the port.
There is a good conversation on how to reduce the STP CPU utilization due to a high number of VLANs configured on a given switch on Cisco's NetPro forum. The following links are referenced in the post (including those links here just for good measure).
http://www.cisco.com/en/US/docs/switches/lan/catalyst6500/