Both sentences are ambiguous in their meaning. They imply that the agreement was NOT to make the down payment, whereas I assume you are trying to inform them that there was an agreement, the agreement was to make a down payment, the down payment has not been made, therefore the company has not (yet) met the agreement. If that's the case then I suggest something like this:
The agreed down payment has not yet been made by your company.
'Yet' changes the meaning in a very subtle way. I would use 'yet' if you want to express that you are still waiting for and expecting the payment to be made.