Ok I believe I have actually found part of the issue I have checked about 40 systems now, and every system not reporting AV being present is running McAfee VSE 8.7i patch 3. Currently our systems are split between patch 2 and patch 3, although current latest version is patch 5.
I tried two tests with interesting results.
1. I upgraded one of the systems reporting AV to TNI correctly from patch 2 to patch 5. It continues to report correctly after a rescan.
2. I upgraded one of the systems not reporting correctly from patch 3 to patch 5, and it continues to fail to report correctly.
I have sent through two xml files for the two machines I updated in the testing above to the email address as requested.