Arduino Due Barebones Issue

Hi,

I built a barebones version of the Arduino Due and am attempting to program both over BOSSA/SAM-BA and JTAG. When I attempt to program over JTAG everything "seems" to program fine with no errors but then my code never executes. Additionally, if I try to set the GPNVM bits (over JTAG) I get this error:

Timestamp: 2015-06-16 19:24:10.738
Severity: ERROR
ComponentId: 20000
StatusCode: 0
One or more registers differs
Atmel.VsIde.AvrStudio.Services.TargetService.RegistersMismatchException:

I plug in my device to the USB port and it gets recognized as a BOSSA device. I should be able to program the Due despite the fact that it's recognized as BOSSA. This is my output when I program the device in the Arduino IDE:

Sketch uses 10,500 bytes (2%) of program storage space. Maximum is 524,288 bytes.
Erase flash
Write 11636 bytes to flash
[ ] 0% (0/46 pages)
[====== ] 21% (10/46 pages)
[============= ] 43% (20/46 pages)
[=================== ] 65% (30/46 pages)
[========================== ] 86% (40/46 pages)
[==============================] 100% (46/46 pages)
Verify 11636 bytes of flash
[ ] 0% (0/46 pages)
[====== ] 21% (10/46 pages)
[============= ] 43% (20/46 pages)
[=================== ] 65% (30/46 pages)
[========================== ] 86% (40/46 pages)
[==============================] 100% (46/46 pages)
Verify failed
Page errors: 46
Byte errors: 11213

I put the output on verbose mode but there are no other details then what you see above.

The only thing I can think of is that my oscillators weren't carefully picked nor are the bypass capacitors. They are, indeed, 12 MHz and 32 KHz just like the Due but not the identical ones. Does that really make a difference?