I close J3 during power-up as I used to do in past but cannot get into SAM-BA mode. What is wrong?

The boot sequence changed some time ago. J3 is used to bypass the NAND preventing the ROM code to load at91bootstrap from that media.
Since the BCH update in March 2013 (see http://armbedded.eu/downloads/Stamp9G20), we do not consider the NAND to be the proper location for at91bootstrap. That is why we switched to the DataFlash which is equipped on all Stamp9G20 and NanosG20 boards since 2013. The DataFlash however uses a different chip select that has to be bypassed to prevent autoboot.
Please see http://armbedded.eu/node/8 to figure out which jumper is used when the DataFlash is used. In case of doubt where at91bootstrap is stored on your board, it is perfectly okay to close both jumpers during boot.