I have a custom AT91SAM9260 and also the AT91SAM9260-EK
I can use SAM-BA via SAM-ICE jtag on both boards
I can use SAM-BA via the DBGU port on the eval board, but not the custom board.

The custom board has:
OSCBYPASS - (25MHz clock on XIN)
OScSEL = 0 (Tied to GND)
No USB port

What else could keep me from executing ROMBOOT and seeing >ROMBOOT spew from DBGU on power up?

You mayneed to do this (maybe in the bootstrap):

Set the MOSCEN bit to 0 in the Main OSC register (CKGR_MOR).

Also check the BMS pin. It needs to beset to 1 in order to boot from internal ROM. I think there are also some POR restrictions on the level of the BMS pin.

Please check in Figure 13-2. Clocks and DBGU Configurations of the datasheet. If you select the internal slow clock, the "ROMBoot" will not display as the DBGU not configured. See Table 13-2, the 25.00MHz external clock source should be ok for DBGU or USB connection. Please double check.

Very helpful to me