Hi,
Apologies for the long delay on this one, it fell through the cracks and I should have addressed it much sooner.
I've identified and fixed the bug causing the category restriction to not work. The commission calculation was failing because of a type mismatch when comparing product categories against the restricted categories, resulting in commissions always being zero when the feature was enabled.
The fix is included in the latest build of HikaShop. Please download and install it from our website, then test the category restriction feature again. Both the global setting and the per-partner override should now work correctly.
Sorry again for the wait, and thank you for your patience.