Прошивайте через bat-файл.
STK500.EXE
-cUSB:000200052026 -dATmega128 -ms -I125000 -e -fD2BF -EFF
STK500.EXE
-cUSB:000200052026 -dATmega128 -ms -I125000 -FD2BF -GFF
STK500.EXE
-cUSB:000200052026 -dATmega128 -I2000000 -ms -iep:\Prog\bin\Debug_isp\EEPROM.HEX -pe -ve
STK500.EXE
-cUSB:000200052026 -dATmega128 -I2000000 -ms -ifp:\Prog\bin\Debug_isp\proshivka.hex -pf -vf