Sounds like you may be experiencing spanning tree (STP) loops / broadcast storm.
Are you splitting up user groups / IP subnets into separate vlans (not using default/management vlan 1 for user traffic)?
Running VTP (enabled) w/consistent VTP domain name & password on all switches? Set (all) switches as VTP servers?
Are your 6509's being used as distribution switches (vs. "core" switches in the Cisco vernacular),i.e., are they
- terminating dual uplinks from access switches (in your closets)?
- uplinks trunking multiple vlans (config'd as ISL or dot1q trunks)?
- providing ports for central servers?
- routing/L3 switching (MLS) by using MSFC's in each?
If so, check or try load balancing vlans by
- assiging one 6509 as the root bridge for half the vlans (or whatever split divides the traffic load best) on that switch, the other 6509 for the rest. Ex: switch A, vlans 2,4,6; switch B, vlans 3,5,7 ("set spantree root"

- setting vlan port priority on access switch trunks to appropriate root bridges (trunk with lower priority value - per vlan - forwards that vlan traffic on that trunk; other trunk blocks unless primary trunk drops) ("set portvlanpri"

Ex: on trunk 1/1, vlan 2 has priority value=1, vlan 3 has pri=32; on trunk 1/2, vlan 2 has pri=32, vlan 3 has pri=1. vlan 2 fwd'd on 1/1, blocked on 1/2 & vice versa for vlan 3.
- do the same for (all) vlans on trunks between your 2 6509 (active) Sup's. Config trunks on both switches the same. If running duals Sup's in each switch, cable 1/1 to 1/1, 1/2 to 1/2.
Hope this helps