When entering prices in a Sales Order, if there is a pricing rule that applies to the customer, and no list price for the item, it is overwriting the price with a zero balance. If there is a list price, it overwrites with that. Shouldn’t manually entered prices override this?
Answering my own question: If a user does not have higher level permissions (Permissions for price on SO are lvl 1) then if that user submits the order, the prices are cleared.