I use the SAM-BA with my new AT91CAP9A-DK board.
First, I tried with the COM1/DBGU port(usb and JTAG unplugged), well, the SAM-BA popped out a Message window showing "Communication Error!".
Then I use the usb and the JTAG to do the connection, in both case no error window popped out, however, SAM-BA's main window also didn't pop out as supposed.
So why didn't the main window pop out, anyone with similar experience or any suggestions?

>>So why didn't the main window pop out, anyone with similar experience or any suggestions?

I've certainly seen SAM-ICE/J-LINKs hang up in this way in SAM-BA. It usually indicates that it can't get control of the board properly. On 9260 and 9G20 designs this can occur if RomBoot isn't working properly, or you have code in the NAND/serial flash. Pull chip select jumpers. Also double check all your jumper settings against the documentation.

Start by getting the most current Segger drivers, ensure that the SAM-ICE has the most current firmware, use the standard J-Link tools to see if it can connect to your board and see your CPU properly. Running jlink.exe should update the firmware.

Make sure you are using the most current version of SAM-BA, you should also try some older versions (contemporary with the board release). Versions 2.8 and 2.9 should support the 9RL board.

Try on a different PC, in case you have PC/OS/driver specific issues.

Thanks a lot! Just as you said, I tried with the SAM-BA 2.9 and it worked!