Obviously can't say for sure what is going on since you don't tell us anything about the equipment you are using. Typically, motherboard trays will have standoffs for all possible motherboard sizes that are compatible, and the ones for other types aren't used. For example, if it is ATX, it may have stand offs for ATX as well as MATX.
If this doesn't help, why not tell us what you actually have?
I have an ATX motherboard. (Asus maximus IV to be specific) It seems like one standoff is too thick and one is too thin.