I'm currently running Orion 8.51 with a single custom MIB poller defined, when this is assigned to a single node all works fine and the data is populated in the graph but if I assign it to more than one node it stops polling that MIB. Any ideas?
You should upgrade to Orion 9.1. Many changes have been done to improve the Custom Pollers. There is a Utility named Universal Device Poller (UnDP) that replaces the File > Custom MIB Pollers menu.
Beside solving your issue you will benefit of all the new features: