It would depend on the load order, bash tags and if you rebuilt your patch after making the change.
I didn't put any bash tags on Level Rates Modified or Smarter Mercantile Leveling because BOSS did not suggest any. But Level Rates Modified x5 was automatically merged. The BOSS suggested load order was Smarter Mercantile Leveling then Level Rates Modified. When there was no change I tried swapping the load order. When again no change I put it after the bashed patch and voila!
And yes, I rebuilt my patch after every change. So having that information does it sound like it was indeed because the Level_Rates_Modified_x5.esp was merged into the Bashed Patch? I'm asking so I understand the mechanics. Thanks alot!