I came across this issue on a 2900 series router with SM-X-ES3-16-P EtherSwitch module. I was initially able to initiate a session using service-module g1/0 session and configure the switch normally. The problem arrose when changing the ROASt configuration to use a different native vlan than Vlan1 (we'll say vlan 30 for the sake of discussion).
So on the virtual interface:
interface GigabitEthernet1/0.30
description /// NATIVE VLAN \\\
encapsulation dot1Q 30 native
service-module time out initiating sessionservice-module time out initiating session
In this configuration, initiating a session from the router fails
The trunk side within the EtherSwitch module had always been set to vlan 30 as follows:
interface GigabitEthernet0/18
description /// TRUNK TO ROUTER \\
switchport trunk encapsulation dot1q
switchport trunk native vlan 30
switchport trunk allowed vlan 2-29, 31-4094
switchport mode trunk
Whith the above configurations, if an SVI with an IP has been configured on the EtherSwitch, SSH and Telnet is are possible from the network side to the switch, but initiating a session with the EtherSwitch from the router will time out. This can be remedied by removing the "native" identifier on the virtual interface for the native vlan on the router as follows:
interface GigabitEthernet1/0.30
description /// NATIVE VLAN \\\
encapsulation dot1Q 30
This surprisingly does not cause any "native vlan mismatch" errors or anything of the sort (although it likely makes vlan 30 irrelevant and could be removed altogether), and you will again be able to initiate a session through the router.
I am assuming the heartbeat for the EtherSwitch is always sent through native vlan 1 so changing the native vlan to anything else doesn't allow sessions to initiate properly. Any input on a better workaround (like how to change the vlan for the heartbeat) would be appreciated. Also, I haven't experimented with allowing the new native vlan on the trunk, but this is unlikely to help since I have never allowed vlan 1 on the trunk either, and it still seems to work on vlan 1.