Hi Darcy,
Even if you compile a .sb5 project, the SetupBuilder 8.1 compiler can only generate Windows 8.1-aware applications (always embeds the IDs for Vista, Windows 7, Windows 8 and Windows 8.1).
Perhaps you double-clicked the .sb6 project and accidentally compiled with the old SB6 compiler? Or your automated build system picked the old SB6 environment. If you still have that old "Uninst_MT.exe" then I can tell you which compiler version generated it.
But I am glad that it's working fine now. Thanks so much for your kind words!
Friedrich