section loading by avr studio

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I'm using eclipse to code, and studio to debug. I have some additional code sections that I have defined, and I have included the arguments in the linker ( -Wl,--section-start=.bootdata=0x1FF6) It compiles OK, and I can see the code in the listing, and map.
But when debugging in avr studio this section doesn't get loaded into the device (using jtag MkII debug wire). I can see it in the hex file, so I'm sure its defined correctly in the elf file. Is this a known problem, or am I doing something inappropriate?

I could program using the ISP mode from the hex file, and debug without loading the code. But this is a pain, since you have to constantly switch the debug wire fuses between modes all the time (atmega88P).