[quote user="Steve Deschryver"] I don't think this is a software issue[/quote]
Perhaps, but I can only help you debug the issue while running Linux.
The reset states of these pins are as GPIOs, so if the LCD is able to run at first, this means that your kernel is able to change the pinmux configuration values from GPIO to LCD function. It's strange that this doesn't happen when you try to reverse the pins states. Can you read back the pinmux configuration registers values and see if they changed?
Best regards,
Miroslav