I have two options to boot with android in bootmenu. For me it's the one that looks like this, that works for me
(external SD, partition 2)
I'm not sure why you have those problems, but if you're not able to boot with non of your options in bootmenu and have to rename files i would reinstall with autoinstaller again and see if that would fix it for you

e: at the moment i can't boot nitdroid cause i flashed another zImage to get my radio working in maemo and that kernel somehow doesn't work on my device to boot nitdroid...

@archimark i had that problem, i had a few before it finally worked for me. Before the autoinstaller i tried with vm linux mint and that didn't work so i partioned my sd card on my N900 and then used the vm linux mint to download and untar the froyo to my sd card and then settup the bootmenu and that worked. After the autoinstaller i've used that
Try to look at this link, the partitioning didn't work for me with this method, but the rest did...
http://wiki.nitdroid.com/index.php?title=N900-install
Somewhere in this thread kingoddball gives a guide on how to partition sd card on N900...
This is how i got it to work, trying different approaches, but i can't say speciffic whats wrong in your end. Sorry...