The setting "Synchronize component items that are not currently present on the monitored device" should only be used if uniqueness can be guaranteed:
From that page:
Synchronize component items that are not currently present on the monitored device When the Data Aggregator finds a device component that is no longer present in the environment, that status of the component is set to Not Present. By default, the Data Aggregator does not synchronize these items because data can no longer be collected for the item. Historical data that has not reached the data retention limit is still available for these items.
Important! If the properties of an active component match the identifying properties of the not present component, the components are indistinguishable. Data from the old component might contribute to group based dashboards instead of data from the active component. Enable this feature only under the following circumstances:
You want to report on historical data for items that are no longer present in the environment.
You can ensure that the not present item does not conflict with an actively monitored item.
You can identify the not present items so that you can exclude the items from groups.
So what is happening here is the Not Present items are conflicting with the active items.
If you un-check the setting "Synchronize component items that are not currently present on the monitored device" the Not Present components would no longer be synced to CAPC and you would be able to report on the active components.
This does not remove the Not Present items from the Data Aggregator.
To permanently remove Not Present components, see: