Setting both the light munich and munich dark as a base malt provides a mash pH of 5.36 on the water calculator which seems right to me.
Looks like some changes to the grain categorization from beta made it to the live site when it shouldn't have.
I spent a good bit of time going over the entire fermentable database, correcting types and categories for better accuracy and organization, and we'll be introducing a couple new ones shortly (specialty malt, smoked malt, honey, fruit juice, and fruit puree).
Unfortunately those changes were supposed to stay separate on beta until the update was ready, so now we're using the live sites pH calculations with the beta fermentable categories, doesn't know what to do with a specialty malt, (which ATM just includes munich, aromatic malts, biscuit, melanoidin and dextrine malts like carapils).