Well I'm not entirely familiar with the software and flash process, but when it flashed mine that was the next thing in the process. When I initially built the circuit I had issues with my watchdog timer circuit resetting itself and not sending out the proper signal. I don't have the log files at my disposal currently, but it would connect briefly and then time out and give me errors. I wish I had an ECU at my disposal right now to see if I can replicate your issue, but I don't.
Opening port 'COM2' ...
Loading Comms DLL
Loaded Comms DLL
Initiating BOOT SCI sequence
Received immediate response from device: 0xAA
Using micro-Kernel : 'C:\Program Files (x86)\Renesas\FDT4.08\kernels\ProtB\7055\Renesas\1_0_00\uGen7055r.cde'
Downloading and verifying micro kernel...
Device is erasing...
Erase Timeout value set to 21 seconds
micro-Kernel download successful
Sending inquiry for getting line size