For a Linux server that you know has LEM agent installed and Asset Inventory is being reported back in SAM, and if you go to the Asset Inventory subview - are you able to see LEM agent listed in the list of installed software? Once we know that, creating a report filter should be easy enough.
Why some nodes are not showing Asset Inventory in the List Resources option - that is a separate issue. Probably an SNMP configuration issue that is not presenting the software inventory OIDs