I've got an MX 84 with an uplink to a Cisco SG500-52P. All routing is done on the SG500-52P with several VLANS configured on that. The MX has a route back to each VLAN.
Existing firmware was way behind, 13.36, but had no issues. After the upgrade there were continued issues with connectivity from the MX to the downstream switch holding each of the VLANs. Checked the event log on the Meraki and see the following :
Since you have narrowed down the issue to be reproduced by firmware upgrade, I would call support and have them working on determining the exact issues and version of firmware that this is happening on.
The other thing I would check is the route table before and after the firmware upgrade.
We just had the same issue with the same equipment. upgraded to 14.40 from 13.33. Rolling back tonight. Wish I had seen this before upgrading the firmware. It was a nightmare coming in on a Monday morning with phones not working.