Reply to Firmware Installation Successful - VCI won't load bootloader

So, I've successfully upgraded the firmware on my VCI-100 to 1.3 (by checking the toggling snap button), which is good news.

Here is the verbose log from FDT:

Flash Development Toolkit and flash programming components
are provided without support

OS: Windows XP [Admin]
FDT API initialised: version 4, 02, 00, 008
Clock Frequency (External) = 24.0000MHz, Clock Mode = 0, CKM = 1, and CKP = N/A
Connecting to device 'H8/3052F' on 'COM7'
Configuration:
'BOOT Mode' connection - using emulated interface
Opening port 'COM7' ...
Loading Comms DLL
Loaded Comms DLL
Initiating BOOT SCI sequence
Attempting 9600
Received immediate response from device: 0xAA
Using micro-Kernel : 'C:\Program Files\Renesas\FDT4.02\kernels\ProtB\3052\Renesas\1 _2_00\uGen3052.cde'
Downloading and verifying micro kernel...
Device is erasing...
Erase Timeout value set to 21 seconds
Erase Successful
micro-Kernel download successful
Sending inquiry for getting line size
Buffer size has been set to default (128 bytes)
Sending selection of device command
Selection of Device - Device selected, code 0302
Sending selection of clock mode
Sending selection of clock mode
Selection of Clock Mode - Clock selected, code 0
Changing baud rate to 38400 bps
Set baud rate value = 38400
Downloading main kernel 'C:\Program Files\Renesas\FDT4.02\kernels\ProtB\3052\Renesas\1 _2_00\Genm3052.cde'
Main kernel download complete...
Connection complete
Processing file :"C:\Documents and Settings\Chris\Desktop\vci-100se_13_firmware\VCI-100SE_1.3_Firmware.mot"
Operation on User Flash
Downloaded the operation module
Writing image to device... [0x00000000 - 0x000000FF]
Writing image to device... [0x00000200 - 0x0000647F]
Writing image to device... [0x00008000 - 0x0000807F]
Writing image to device... [0x00009000 - 0x0000907F]
Writing image to device... [0x00009080 - 0x0000917F]
Writing image to device... [0x00009180 - 0x00009AFF]
Data programmed at the following positions:
0x00000000 - 0x000000FF Length : 0x00000100
0x00000200 - 0x0000647F Length : 0x00006280
0x00008000 - 0x0000807F Length : 0x00000080
0x00009000 - 0x0000907F Length : 0x00000080
0x00009080 - 0x0000917F Length : 0x00000100
0x00009180 - 0x00009AFF Length : 0x00000980
27.75 K programmed in 34 seconds
Image successfully written to device
Disconnecting
Disconnected

But I've got a new problem now, the bootloader which loads the drivers in Windows now doesn't work, so the device isn't present in my system anymore when I power it on (meaning windows doesn't recognize it).

Has anyone seen this before?

Cheers
CM