I have come across this issue several times especially when brake lines have rotted. When the brake maste cylinder becomes empty, most often times the brake hydraulic unit has air trapped inside of it. To make the brake pedal hard again, this is what you must have done to correct this concern.

Attach a pressure brake bleeder device to the vehicle. Here are some tools you will need.

Blue Point Brake Bleeder - BB100C QTY 1
Blue Point Pressure Cap - YA8925 QTY 1
BMW Brake Fluid DOT4 - 81220142156 QTY 4
Catch Pan for brake fluid and or Gatoraid Bottle with vaccum hose.
11mm and 13mm Combo Wrenchs

Assuming you have already bled the RR, RL, FR, and FL circuits sucessfully. The next step is to bleed the master cylinder. Gain access to the brake lines coming and going to the master cylinder, and carefully brake open the lines for a few seconds each. If you see bubbles coming out, then that is a good sign.

Next you must move on to the brake hydraulic unit. Gain access behind the drivers headlamp. It may be easier to remove the headlamp and or 3.0 Airbox. Do the same for the brake lines coming and going from the hydraulic unit.

Now the brake pedal should feel firm, and no longer fall to the floor after starting the vehicle. If however this does not correct the issue. You must attach the BMW DIS/ISTA D to perform service function to cycle the solenoids in the ABS module. This should free up any trapped air bubbles. You can leave the pressure bleeder on the vehicle while is it being performed. After this procedure, perform a regular brake flush again.