I cannot seem to get the sam-ba_cdc.exe GUI to recognize the SAM3S4B processor on our board using the GUI (connected via USB).

Either it will not recognize the COM port that the SAM3S is connected to (despite enumerating properly according to the device manager) or will simply quit working once the proper COM port and SAM3S4 evaluation kit has been selected and connect has been clicked (no error message).

The SAM-BA works with our SAM3S-EK board

What is making it fail on ours and how we can fix it?

The two biggest differences I can think of are we are running on a 16MHz crystal unlike the EK's 12MHz and we are using a SAM3S4B processor not a SAM3S4C.

Could either of those be the problem? If so what do we do about it?

Since you did not mention it, the obvious question is: what is the operational state of your SAM3S4B board? What on the board does seem to work?

Regards

Everything, pretty much. I can communicate to it via USB when I program it over JTAG. But when I erase it to set it back to the bootloader, it enumerates but for some reason I can't get it to work with the software.

FWIW it is an engineering sample part.

Did you solve the problem? I have the same issues. The USB Bootloader enumerates:

olaf@pc:~$ lsusb
...
Bus 001 Device 016: ID 03eb:6124 Atmel Corp. at91sam SAMBA bootloader
...

But sam-ba hangs when i try to connect to it. It does work with the sam3s-ek.
We also use the sam3s4b with a 16mhz crystal.

I believe the problem is to do with the 4k 'applet' that SAM-BA uses to talk to the flash memory. I believe this is starting and switching to the external crystal and therefore changing the baud rate. How to do this is covered in C:\Program Files\ATMEL Corporation\SAM-BA v2.10\documentation\CustomApplet.txt (section 3), although it doesn't mention changing the crystal as a reason for needing to re-complie.

Chris