Well Linux was the solution to solve my problem, it worked just fine without any issues.

I write here the basic steps just in case someone else got a similar issue:

1. Get a Ubuntu Live CD (Just download the default Desktop version) and burn it on a empty CD

2. Get the .tar.gz version of the flasher from http://tablets-dev.nokia.com/maemo-d...-downloads.php and download the related firmware from http://tablets-dev.nokia.com/nokia_N900.php

3. Move the downloaded files on a USB stick or something similiar, you can unzip already the .tar.gz file and put all files including the firmwares in the same folder.

4. Boot from the CD (You may need to set your CD drive as first boot device) and select "Test Ubuntu (Live mode)".

5. Open a terminal and linux and open your USB stick (Probably in /media/<stickname>/...)

6. Use the command "sudo ./flasher-3.5 -F <firmware-image> -f -R" to flash your device, it seems to be better if you flash the eMMC image first. Be sure that you start the flasher first and connect the phone afterwards, it will detect it just fine then.

That's it, everything worked fine for me in a few minutes.