What can I do to try to troubleshoot RPC Server issues when auditing machines running Windows 2008?

There are two ways you can fix this :

Enable RPC permissions in the Domain Group Policy: 

1- Run Microsoft Management Console on a Windows XP machine (Start|Run|mmc). 

2-Add "Group Policy Object Editor" snap-in (File|Add/Remove Snap-in...|Add...|Group Policy)

3-Select the Group Policy Object for which you want to enable RPC ( Normally this will be the "Default Domain Policy", but if you already have other Group Policy Objects enabled for your networks, select the appropriate one ) 

4-Navigate to: [Group Policy Object]|Computer Configuration|Administrative Templates|Network|Network Connections|Windows Firewall|Domain Profile ( for a Domain administered network - Standard Profile for a Workgroup network )

5-Edit Setting: "Windows Firewall: Allow Remote Administration Exception"

6-Set "Enabled".

7-Set "Allow unsolicited incoming messages from:" to "localsubnet" (without the quotes)

8-Apply settings

These settings will not generally take effect immediately. You can use Microsoft's Group Policy Update Utility to force immediate updates ( see Microsoft's article: "A Description of the Group Policy Update Utility" )

Enable RPC permissions on a single target machine: 

1- Run Microsoft Management Console on the target machine (Start|Run|mmc)

2-Add "Group Policy Object Editor" snap-in (File|Add/Remove Snap-in...|Add...|Group Policy)

3-Select the "Local Computer" Group Policy Object for which you want to enable RPC 

4-Navigate to: [Group Policy Object]|Computer Configuration|Administrative Templates|Network|Network Connections|Windows Firewall|Domain Profile ( for a 5- Domain administered network - Standard Profile for a Workgroup network )

5-Edit Setting: "Windows Firewall: Allow Remote Administration Exception"

6-Set "Enabled".

7-Set "Allow unsolicited incoming messages from:" to "localsubnet" (without the quotes)

8-Apply settings

These settings will not generally take effect immediately. You can use Microsoft's Group Policy Update Utility to force immediate updates ( see Microsoft's article: "A Description of the Group Policy Update Utility" )