I have had similar luck using the AVR dragon to program targets from bascom using EVI 287's process
However instead of using the avrdragon.exe command interface i am utilising the atprogram.exe command line interface that comes with atmel studio 6.0 and have modified the text file accordingly
[b:241548b715]"C:Program Files (x86)AtmelAtmel Studio 6.0avrdbgatprogram.exe" -t avrdragon -i ISP -d %1 program -c -fl -f %2[/b:241548b715]
Obviously your file path may be different however this is the default installation location for atmel studio 6.0
the -t command specifies the programing tool. In this case the avrdragon however this process will also work for the stk500 jtageiceX 8 different tools in total
-i specifies the mode, in this case ISP but you could not doubt use jtag or debugWire if you prefer
-d specifies the device. So moving from chip to chip you will need to modify the settings as per Evi287's notes however i dont find this to be a big inconvenience.
the program command commences programing operations (no surprise there)
-c performs a chip erase
-fl specifies programing flash address space
-f specifies the file
There is a lot more options you could potentially explore with these commands, running the application atprogram.exe with no commands will display help information and provide further options.
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