I work with the individual reporting this issue and turns out a bad line card on the 6509-E where these 4948e access switches trunk to is the ultimate root cause. I don't believe there were any syslog or other indicators of the failure and it was semi-masked by the fallout being dependent on where the VLAN roots were homed so it wasn't consistent. Ultimately when the VLAN roots were reviewed in-depth, it did make complete sense on the impact being seen on just some access switches and ports and not others. I believe I've written up all the pertinent facts here or perhaps left a few out and they will be filled in or corrected later.
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