Nios behaving erratically?

It's not plain as day to me what could be the problem except for that "got_out_data". I don't see anything but an assignment of 0 to it.

Also this line:

data[0] = IORD(USB_SX2_BASE, 0x00);

Since it's a hard coded access you may want to declare "data" as volatile. The compiler may see that and say "why should I keep stuffing data into "data[0]" it should have it from the first time".

If this is indeed the problem I bet this will work (not pretty but the compiler can't break it):

IOWR(USB_SX2_BASE, 0x02,IORD(USB_SX2_BASE, 0x00));