I am having issues with my Altera DE2 board. I have developed a NIOS II softcore processor with two PIOs. One is an input from SW[7..0] and the other is a 12bit output. During the inital testing phase I wired the outputs to LEDR[11..0], and everything was fine and dandy. Code ran flawlessly. Great, now onto the next stage. All I did was change the outputs from LEDR[11..0] to "GPIO_1,GPIO_1,GPIO_1,GPIO_1,GPIO_1,GPIO_1,GPIO_1,GPIO_1,GPIO_1,GPIO_1,GPIO_1,GPIO_1". I had to only use the even pins because of the way my cables connected to the board. I skiped GPIO_1 because it is a ground. I recompile the quartus project, load the sof file onto my DE2, load the .elf file back onto the board. I expect the outputs that I was seeing on LEDR[11..0] to now be on the JP2 pins. Problem is it isn't. I run the code...and random leds on the board start blinking instead. (I see LEDR17, LEDR8, LEDR9, and even some of the 7-segment LEDs). I know the pin assignments are correct because I used the .csv file supplied by Altera. I have no idea what is going wrong. Any suggestions/ideas?