Hi Lukas,
I've successfully programmed a 4 MB Macronix MX25L3205D serial flash with SAM-BA and a AT91SAM9G20. I was able to put AT91Bootstrap, U-boot, and the Linux kernel all in the serial flash and boot each in sequence. I didn't have to do anything unpleasant to the applet to make it work.
I previously had some trouble with an SST serial flash, so I spent some time probing the SPI lines and digging around in the applet source. Here are a few relevant posts that cover some of the stuff I did:
viewtopic.php/f,9/t,19628/viewtopic.php/f,26/t,19621/viewtopic.php/f,26/t,19615/Feel free to contact me if you're stuck. I believe my contact info is findable on the internet.
Brandon