We have a a good number of EX2200 switches. We've observed issues when the switch boots from the backup partition (which, unfortunately, happens all too often when we restart our EX2200s).
Things like aggregated links may not function at all, or LLDP won't be started (despite the config clearly calling for AE interfaces and LLDP on all interfaces). This is even with a MATCHING version in both partitions. The switch boots from the backup partition just fine, and has a good config, but certain random services just don't start.
This occurs on both our EX2200 switches setup in VC, and standalone switches. This also occurs with versions 12 or 15 (yes, I know they pulled 15, and we are working on downgrading all of them to 12).
I've searched all over for information on this behavior, but haven't been able to find anything about missing functionality/services when booted from an equivelent backup version. I'm hoping someone can help point us in the right direction.