I can't seem to find any setting that will let me disable the Logical discrepancy for "Trunk VLAN Mismatch" ?
from the CiscoWorks home page go to
Campus Manager > Administration > Network Discrepancy
click on 'configure' and drill down to Discrepancy-Vlan-Link and remove the mark from 'Multi';
use the online help from LMS to get details about the messages:
(btw,myself, I found this message very helpful)