DE2-115 USB ISP1362 Problems

I've started designing firmware for the ISP1362. I've run into a snag which has confounded everyone I've talked to. I wrote the hardware abstraction layer (HAL) and it worked perfectly. This is the block that toggles the I/O when I I give it an instruction (read, write data, write command) and a value. When I modified a different part of my design it broke the USB interface and I don't know why or where. If you look at the two attached screen shots you'll see that the I/O experience the exact same values and timing. Except, one is working and giving me the chip ID of 3630h, and the other isn't (0000h received).

Has anyone run into such an issue in Quartus II? What about with this USB Chip? If I'm not messing with the HAL, how can I 'break' the design?

i'm using 12.1 Web/free Edition.

Thanks,

-Joe