If you are scanning thin clients, you might need to disable SSH on the affected IP range (you can do this under
Configuration\Scanning methods, section
IP Address Range scanning) and scan the asset with SNMP. That should provide the correct MAC address. Lansweeper uses the MAC address of the network interface used for scanning as unique identifier. From what you describe it seems that the Linux machines provide virtual MAC addresses. SNMP needs to be enabled on the thin clients. Details on how to scan network devices can be found in
this KB article.
Note: Lansweeper reads the MAC address of network devices from ARP tables if the scanning server is in the same subnet as scanned devices. If you are scanning other subnets, that won't work any more.