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AD User Groups Listed (Sometimes) But Do Not Work

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Good Morning Guys / Niall -

I need help with an important issue, please. Our domain currently has numerous AD Groups for both devices and users. Our SCCM environment (2012 R2 SP1 CU3) has discovery set to add all of them and the default user collection "All User Groups" has 6,396 members from which I may search and locate individual groups.
However - when adding a query to add a user group to a User Collection (or group with systems to a Device collection); none of the members are added to the collection. Below is the statement used which I typed in to directly specify the group:
select SMS_R_USER.ResourceID,SMS_R_USER.ResourceType,SMS_R_USER.Name,SMS_R_USER.UniqueUserName,SMS_R_USER.WindowsNTDomain from SMS_R_User     where SMS_R_User.UserGroupName = "company\\ABQ-Techs"
If I choose to build the query via wizard, choose User Resource, User Group Name, then click Value (which should list all User Groups), only about 10 are listed - perhaps less than a percent of the ones we have. The same applies to Device Collections as when I try to create a query to include devices in a collection and click Value after setting "Security Group Name" or "System Group Name", I get just a handful of items to pick from.
I found that this post describes the exact same issue, but there's no resolution listed despite many seemingly having the issue. All discovery properties are basically at defaults and logs don't seem to show any errors.
I just ran a full discovery then edited a copy of the log to include only events during the process plus change sensitive info which is attached.
Any suggestions? Thanks!

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