niosII development board download problem

This is an Altera board? Maybe the boxes are mislabelled (I have seen the new 2s60 board and they do have a fan on them so that's why I think it's just the box being wrong).

Judging by the time stamps you are seeing, you have downloaded hardware that has an old SOPC Builder instance, then compiled software for a newly generated SOPC Builder system (I'm talking about the "ptf" file by the way).

When working with the reference designs I recommend this:

1) Copy the hardware design to a "work" folder (that way you don't mess up your only copy of the hardware)

2) Modify, regenerate, compile....etc this copied design only

3) Base your software projects off the ptf file in the copied design folder (I'm guessing you have moved hardware around but didn't point to the same files in the IDE).