So I noticed that intra-vlan network performance had decreased significantly recently but the effects were sporadic. Wireshark traces showed a lot of traffic bleeding over from multiple vlans and file copy performance between vlans was a staggeringly low. I ran the a cable qualification device on all the links and tested the speed between each switch. Everything was fine as long as I didn't do an inter-vlan activity. So I knew then that the problem was in the 6224 which I use for my layer 3 switching between vlans. While trolling through forums, I noticed someone had recommended STP as a place to start in troubleshooting. I set my 'root' switches priority 8192 (lower is higher in priority) and all the issues disappeared within a few seconds.
As far as I can tell the Multiple STP operation mode was running into problems when a load was applied. Since all the other switches are by default set to 32768 by default, now I shouldn't have this problem again.