Are you checking the temperature of the mixture to make sure you heat it to the correct temperature?
When the custard becomes watery, it means it wasn’t heated to the correct temperature.
Depending on the recipe most need to be heated 175°F – 180°F.
If the recipe contains cornstarch, the temperature is higher, 212°F is required for proper starch gelatinization to occur.
A starch like wheat flour has a lower starch gelatinization temperature, no more than 200°F.
Starch gelatinization occurs when the starch molecules absorbs water. At a certain point it absorbs so much water it actually burst. The contents (amylose and amylopectin) then mix with water molecules and essentially immobilize the water molecules. That’s what causes the thickening.
All starch gelatinization breaks down over time. It’s called retrogradation. When that happens the water molecules are released from the suspended state. When the starch gelatinization mass is made really robust, retrogradation happens very slowly.
Your custards are just reverting to retrogradation too quickly, most likely because of improper cooking techniques for the type of starch used.