I'm going to manufacture few pieces of Due PCB boards, but I'm really confusing about this above. The small chip 74LVC1G125DCK has been moved to left bottom corner. Seems that's the right position.
The current EAGLE file released on Due production page matches the second one board in that picture. So it's not the latest one.
Hope Arduino team release the latest one soon.
There are more diffs:
- above the ISCP from the 16U2 are the Solderspots named for Aref Intern or extern
- near the TWI pins the JTAG header is present not only the holes
- left from the SAM the external crystal (Y2) for the RTC-Modul is missing
Think thats all at the first view.
The position of the little IC is in my opinion not worse but the crystal for the RTC would be nice to have, the labeling from the Aref is nicely