Emby stated there was a new version yesterday so I forced update to that I'm now on 3.0.5986.0 I no longer get the too many open files error but the program stops responding after "awhile" and I'm forced to restart it in OMV by turning the plugin off, saving the config change, accepting the change then turning it back on, saving, accepting. Just clicking restart doesn't seem to do anything. Nothing else has been updated so I'm guessing the issue is still with mono.
On a different note for the mods I think the reason my account was being banned was due to my VPN end point getting flagged for spam. I've switched end points now.