Hi @kyohei ,
After downloading, KinetisFlashTool will reset target. And the MCU will read FOPT and then, if execute ROM bootloader, it will read BCA. So, you can
1. disable ROM bootloader by FOPT[BOOTSRC_SEL], or
2. If you want to keep ROM bootloader, you can set a short timeout in BCA, or
3. If you need a long timeout period, you have to use blhost.exe instead of KinetisFlashTool. Please refer to Table 13-2 in reference manual. ROM bootloader support 'Execute' command which can run user application code. But KinetisFlashTools doesn't support it. You can use blhost to download and execute.
Regards,
Jing