The interesting part is that the server that plugged into that interface has no OS on it. I would expect some DHCP request coming because of the default server interface settings, but not to make spanning-tree converge. I don't think that server caused the problem, however, when we disabled the interface the problem seemed to stop. But when we enabled the interface again to get some captures from it the problem did not come back.
SO that server caused a bunch of TCNs which in turn caused STP instablity. One thing - you said server has no OS - why do you have then have trunk to it and allow multiple VLANs there?
I would consider this configuration having switch on the other side - or server emulating switching software or VMware to use those VLANs.
It definitely smth starting to happen on the server side and 4948 was getting TCN BPDUs from it thus re-sending it further f port was not just flapping). Also this command on Gi1/13 - " spanning-tree portfast" - Ithink that should be "spanning-tree portfast trunk" on trunk port. Thats why I guess that did not help to stop TCNs as portfast actually help to avoid those.
The server is a standb alone server. We were thinking that it is a VM box, but the server guys said it is not. The server used to be connected to this port was a VM box, that is why it configured as it is. The intersting part is that when we turned the port back to capture the traffic the issue we had did not come back and all I saw in the capture that the server tried to get an IP address from the DHCP server. After the interface was re-enabled the spanning-tree convergence did not happen, that is why I think something else was causing the issue.
Difficult to say now - can only guess and this is not good approach for troubleshooting. On reoccurrence - I would again check the STP TCN to find where those are growing from - and sniff that port before shutting down. Also CPU usage, show log on the switches in path can be helpfull.
We are pleased to announce availability of Beta software for 16.6.3.
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