with sam3s2b in certain cases, when you load the program which will very soon becomes waiting for slow clock to stabilize - and there is no crystal on the board - it becomes stuck: neither flash load works anymore, nor Erase signal applied properly works! This was reproduced on several sam3s2b boards, on which slow clocks are provided by on-board peripheral which hasn't be configured properly to generate slow clocks.
if you run in such troubles as I did, the solution is to conenct external 32kHz signal to the XIN32 pin (I made one from 74hc14, crystal and few resistors). This will make Erase to work again and/or flash load to works.
Not sure if this problem is only on sam3. Please put a feedback here with your experiences.