How many HRUs are you running, and what is your computer specs you are running? I'm in the process of setting up hydroblocks as well. #of HRUs could potentially cause this.

I'd check alignment of your DEM, masks, soil, and vegetation raters as well to make sure they are aligned. Also make sure the grids are aligned too, and your projections are right. I'm sure your data sources look much different than mine given you are looking a the Kaledhon region!