I would suggest starting to tune the settings in fr/flex then, because you're not doing something right. I'm oom every single fight and that's actually a good thing. Make sure your HL, DL, FL, and HR spells are at *reasonable* values, and adjust them multiple times to perfect it.
The Malkorok fight itself is a tricky one for any pally - it's all about shields. Personally, if my CR is spamming anything besides HR I know somethings wrong, because thats how 5.4 hpals should be healing. You could actually be running into an issue with HB itself as well...if you notice the CR stopping the use of HP, i'd suggest closing it and reloading it, manually healing while it reloads.