When Azure VM Scale Sets configuration changes, the updates are not automatically propagated to all nodes, which means there might be temporary configuration differences between various nodes in the Scale Set. To update the configuration, it's necessary to re-deploy the node. 

CloudMonix by default automatically detects changes in configuration and propagates it to all nodes. It's possible to disable this option by ticking the checkbox in the Azure VM Scale Set configuration dialog:

Keep in mind that if the auto-update option is disabled, then of the configuration changes CloudMonix may not be able to capture some of the expected monitoring data.