STM32FDISCOVERY netmf 4.4 Clocks

I am currently writing a SDIO driver for the STM32F407VG on the DISCOVERY board. I have noticed
that the example SDIO driver produced by the STM32CubeMX software initializes the the STM clocks
to use the internal 16MHz (HSI) clock. Nice and simple. But the Bootstrap code for the STM32F port for
netmf (C:\dotNet44\netmf-interpreter-dev\DeviceCode\Targets\Native\STM32F4\DeviceCode\STM32F4_Bootstrap\STM32F4_bootstrap.cpp)
use the internal PLL circuit whose input is from the 8Mz external oscillator.

I am wondering what the advantage is of using the internal PLL circuit is opposed to the internal 16Mhz is?

The main reason I am asking is I am stumped. The example SDIO driver generated with the CUBE software works
fine, however when I flash the netmf 4.4 with my driver my communications with the SD card timeout.
The only difference I can see so far is how the system clocks are setup.

thanks for any hints!
cheers