If the item you are editing has a shift level (where it prompts for a size choice), you must have prices in the modifier price levels as well.
For example, the item name of "Pizza" with a SM and LG shift level, the Pizza turns into a new item of SM Pizza and LG Pizza. If you do not have prices within the price levels on the toppings, the software does not know what prices to use.
If your toppings only have one size, you can put the prices in the regular price and the Price Level 1, and set your menu item to look at the Price Level of 1 on all sizes.

