Custom made PCB problem after lost power supply
I suspect the 100k on BOOT0 is not pull-down enough. In the newer F4 series the BOOT0 pin also serves high voltage programming supply (Vpp). 

On the demo boards they hard tie BOOT0 to ground without pull-down, or use a 10k resistor.

Maybe you can measure the leakage from BOOT0 to determine the highest possible resistor.