Ok.. No need to panic at all... I assume you are not having Nokia PC Suite installed on your machine. May sound really crazy (You may call me crazy too, but doesn't matter as it worked for me. lol) but it seems that while flashing eMMC, the N900 goes from Update mode to PC-Suite Mode. In order to proceed, it requires the Nokia Cable Connectivity Drivers which is a part of Nokia PC Suite.

Heed my advice:
Format the device from scratch from the guide exactly as it says after installing the PC Suite. Trust me, I have gone through the same.

Now as you have stated that it is Vista, please do note that 64bit OS cannot flash the device. Therefore, if you are using Windows Vista x64 (Check by right clicking My Computer and clicking Properties) you'll need to either use a Windows XP machine or else you'll need to install a Virtual machine with XP on it.

(If you are using Windows XP Mode or something. If so, install the PC Suite on your XP Mode machine and make sure to click the USB menu on top and select the N900. May need you to do it around twice as it changes its modes from update mode for the first part and then to the PC Suite Mode in the eMMC flashing.)

Do notify me once you get through with these steps. If it still doesnt work out, I would try assisting furthur.