Multiple Domain Inventory Scan

We have multiple domains which have two way trusts that we scan. If we scan a domain that the SD is not a member of, the domain scan fails. If you scan an individual machine using the FQDN such as machine.remotedomain.com it works...but if you use machine name only but set the domain name to remotedomain in the Domain Name field and set the scan type to Domain - it fails. So when you do a "NEW SCAN", if it looks like this:

Workstation Name / IP = machinename.remotedomain.com
Scan Type = Domain
Domain Name / Network = REMOTEDOMAIN

it works...but if it is set to the following, it fails. Any ideas?

Workstation Name / IP = machinename
Scan Type = Domain
Domain Name / Network = REMOTEDOMAIN