I have a really interesting question right here, it happened to me yesterday morning and trying to find any explanation was a bit difficult for this matter, maybe some of you guys could help me, here it is:
I had to add three VLANs to a medium sized switched network which had a quite big number of vlans for the size the network was (63 vlans) and I added them in the VTP Server switch for it to propagate them throughout the network. The thing is that two switches in the network were completely out and they were not communicating with anybody and could only see the CDP neighbor table, no telnet, no ssh, no ping, it just wasn't answering.
Knowing the fact that the switches that get to the maximum number of vlans configured (64) turn themselves into VTP Transparent mode doesn't mean that the switch will not communicate with anybody in the network and it does not reset the revision number, so there had to be something else here that affected the switch. I know that my configuration was the starting point but I believe that there was something in the switch previously configured that caused the outage.
The network was working fine until I made this configuration, so the first two thigs that you suggest were configured correctly also it did propagate correctly because when I looked into the switch it had 63 vlans and only one was added through VTP and it turned to VTP Transparent when it reached it's maximun (64).
Now, it could have been something about the native vlan but once more, the network was working perfectly just before I made the changes.
I believe the switch supports more than 64 VLAN's I think you ran into a spanning-tree problem as the switch only supports 64 spanning-tree instances but support 128 or 250 VLAN's. So if you have PVST running it would have caused your issue as it could have caused a routing loop. See below..
Catalyst 2950 switches that run the standard software image (SI) support 128 VLANs; Catalyst 2950 and Catalyst 2955 switches that run the enhanced software image (EI) 250 VLANs. For the list of switches that support each image, see the release notes. VLANs are identified with a number from 1 to 4094. VLAN IDs 1002 through 1005 are reserved for Token Ring and FDDI VLANs. VTP only learns normal-range VLANs, with VLAN IDs 1 to 1005; VLAN IDs greater than 1005 are extended-range VLANs and are not stored in the VLAN database. The switch must be in VTP transparent mode when you create VLAN IDs from 1006 to 4094.
The switch supports per-VLAN spanning-tree plus (PVST+) and rapid PVST+ with a maximum of 64 spanning-tree instances. One spanning-tree instance is allowed per VLAN. See the "Normal-Range VLAN Configuration Guidelines" section for more information about the number of spanning-tree instances and the number of VLANs. The switch supports IEEE 802.1Q trunking for sending VLAN traffic over Ethernet ports.
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