Could you please clarify the life-cycle of the "probematic" adapter instnace, particularly
Did you created it from scratch and configured with the custom created config-file?
Or this adapter was running fine with the ootb config file and than you changed the config?
When changing the config file, did you stop-change-start the adapter instance?
The Federation adapter log may give more insight to this situation:
Administration -> Support -> Logs -> Master (I suppose Federation vROps has a single node/collector) -> Collector -> adapters -> FederationAdapter_<adapter_internal_ID>.log
The adapter internalD could be find from Administration -> Configuration -> Inventory Explorer -> Adapter Instances -> Federation Adpater Instnace (the "Internal Id" column may be disabled by default, you may need to enable it).
The two that are working were created with the default.
The two that are not i created a new one then added the adapters. I have even stoped the adapter, reconfigured it and restarted the adapter. I have even taken the cluster offline and online again.
I will get a look at the logs soon.
 2018-10-22 07:35:19,648 ERROR [Collector worker thread 5] (3581) com.vmware.adapter.federation.FederationAdapter.onCollect - Configuration file validation failed.: ConfFileValidationException: cvc-complex-type.3.2.2: Attribute 'link' is not allowed to appear in element 'Metric'.
 2018-10-23 04:43:19,422 ERROR [Collector worker thread 11] (3581) com.vmware.adapter.configuration.ConfigurationParser.validateXMLSchema - Failed to validate configuration file: SAXParseException: cvc-complex-type.3.2.2: Attribute 'link' is not allowed to appear in element 'Metric'.
 org.xml.sax.SAXParseException; lineNumber: 5; columnNumber: 107; cvc-complex-type.3.2.2: Attribute 'link' is not allowed to appear in element 'Metric'.
 at org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source)
This is the config file
<?xml version="1.0" encoding="UTF-8"?>
<Metric attrkey="Super Metric|sm_aec7b88f-ccf1-45b3-900f-ccb1dae5aa84" label="" unit="" yellow="" orange="" red="" link=""/>
<Metric attrkey="Super Metric|sm_005a1226-6c2a-4787-b6ab-8015f4d07179" label="" unit="" yellow="" orange="" red="" link=""/>
Is it because they are SM
After reading the log it turns out that 7.0 added the link="" to the end of the metric config. Once i removed it from my config file it worked.
It looks like you have vRealize Operations 7.0, but still using Federation MP compatible with earlier version (I suppose Federation MP 1.0.x).
Once you upgrade to the supported version, you will no longer need to do manual change.
This is addressed in upcomming Federation MP 1.1 release. And this is the version compatible with vRealize Operations 7.0.