I read this item with interest - I was having the same problem, invalid boot.ini. The suggestion from cmay - copy and paste the file - worked for me.
However, in the process of searching for an answer on my own, I find that my sysedit in unable to open either the config.sys or the autoexec.bat files. Perhaps this is related to the boot.ini problem? I tried to copy the files from C:\windows\command\ebd to C: but this did not fix it. Any ideas?
One other observation - I first noticed the 'invalid boot.ini' problem right after installing an upgrade to Nero that required a reboot. Is that how the problem started for others?