What does the configsdump look like? That perk has more than one effect group so that might be adding it to more than one or something.
Could try appending your new stuff as a new effect_group instead of adding it to the current ones. Maybe something like:
<append xpath="/progression/perks/perk[@name='perkBrawler']">
<effect_group>
<requirement name="ItemHasTags" tags="perkBrawler"/>
<passive_effect name="StaminaLoss" operation="perc_add" level="1,5" value=".2,1" tags="secondary"/>
<passive_effect name="BlockDamage" operation="perc_add" level="1,5" value="2,10" tags="secondary"/>
</effect_group>
</append>