Please review this Cisco document regarding interface persistence. This is likely the issue you are seeing, not a problem with Observium itself.
http://www.cisco.com/c/en/us/support/docs/ip/simple-network-management-protocol-snmp/28420-ifIndex-Persistence.html
There is a command you can include in your configuration that will keep interface numbering persistent across reboots. I just don't recall it exactly off the top of my head, or I would include it here.
... Ron