PinMux Utility 1.0.4 will assert DEN call into the saved (pinoutput.h) clearing the GPIO Digital Enable (DEN) bits for the ADC Analog peripheral selected inputs. This DEN function appears to be ok if using the PinMux utility though otherwise falls short to set the DEN bits accordingly.
Appears Tivaware uses GPIOPadConfigSet() to clear the DEN bits register 0:0x51c when setting the pin type as STD such as a PWM output requires, questioning if this is occurring when the GPIO PAD pin type is configured as ANALOG?
This issue is (gpio.c) function in Stellarisware would automatically set the DEN bits in register 0:0x51C accordingly when ever the GPIO pin DIR mode was being set to HW. That functionality is perceived to be missing from call GPIODirModeSet() asserted from within GPIOPinTypeADC().