Device not found on Com port

So I uploaded Blink through the native port, worked no issues. However I choose not have the USB ports power the board due to lack of current needed. So plugging the into the programming port will not power the board. But I did try applying 5v to the ICSP header and that powered the board and blink was working. I have attached what the pcb looks like around the 16u2 and the programming port.

Another thing I noticed not a big issue but I pulled the hex file off the 16u2 and it was different then the one I uploaded. Are they supposed to be the same or is that ok?
Thanks
James

PCB.zip (1.18 MB)