Commerce Price Table: What would cause sporadic zeroing of prices when adding to cart?
Obviously, something is wrong somewhere when the rules are firing to apply pricing. Read up on debugging rules and you'll likely find your problem.

One thing you may want to consider is just writing your own custom logic and then creating a new rule to call your custom logic, bypassing the logic of Commerce Price Table. You'll likely need to really spend your time adding your logic to commerce_price_table_get_amount_qty since that's where the actual field and price get determined.