JirkaL

Just for clarification for others in case they encounter this issue: unknown state indicates that for specific application version ESMC is not yet aware of it's state. This normally happens when new version of application is seen for the first time and it should be resolved automatically in no more than 1 hour.

I would recommend to start by checking whether ESMC Agent installed on client machine is actually connecting to ESMC. For this purpose please follow troubleshooting part of documentation - especially status.html log present on client machine might be helpful in this case.
In case ESMC Agent will be connecting to ESMC, most probable issue is that is is using different name in ESMC or is located in different group, which prevented ESMC to remove "dead" duplicate that is rendered as unmanaged.
In case AGENT is not connecting to ESMC, it is crucial to resolve connectivity issues as described in referenced documentation.

Hello Jirka,
For the first problem, I would first apply "reset the RD sensor database" task, to validate whether the white-list is working (as once reported the data are kept, even in case the RD sensor whitelist is actually working). Alternatively, I would uninstall the RD sensor at all, if it reports too many false positives.
With regards to the second problem, I would recommend to contact your customer care, as the error is generic, and does not give is exact reasoning for what might be the failure. 
Regards,
Michal