Nexys 4 DDR doesn't load bitstream from microSD card?
There's an open source FAT library called DOSFS that's used in a lot of embedded systems / development boards that seems to struggle with some allocation sizes. For Windows using the /A:32K (or as per you comment 16K) format switch to force the allocation unit size seems to fix it, it seems this board suffers from the same problem and probably uses the same library.

I encountered a similar problem a while back on an STM32 based project that used to work when the cards were formatted under Windows XP but it stopped working when formatting under later Windows versions so it seems the default allocation unit sizes used by newer operating systems has changed.