When I placed my order for Marvin windows at a building materials store I paid 50%.

50% for materials

Because windows are custom manufactured it's not unusual at all for a contractor to require a sizable deposit. Around here, 50% down with the remaining 50% due upon completion is the norm.

Purchase only 50% down balance on delivery.

If he is going to steal 75% , im sure he would steal 30 or 50% as well.
No one in his right mind would order custom windows without a substantial deposit.

Box stored are payed in full upfront.

Excellent point by Todd, and this is not inconsistent on many custom-ordered items whether they are building materials or not. Many require full payment upfront, with the minimum (and often the norm) being 50%.