BAD HARDWARE WEEK

It might appear from the installer log that we made the mistake of explicitly deleting \boot.ini instead of just boot.ini. The former would delete the file from the root of the current drive whereas the latter would only delete from the current working directory. It is not quite so; the mistake was to assume that the file would be deleted from the current working directory without giving the full path. In fact, this is the code in the installer script that caused the problems:

Section "EVE-ONLINE"
SetOutPath "$INSTDIR"

Delete "boot.ini"
Delete "manifest.dat"

File "boot.ini"
File "manifest.dat"
File "resDX9*.stuff"
SectionEnd

Guess is this a part of Vista application software ?
The documentation for the Delete function says the file should be specified with a full path but in fact it must be specified with a full path, like so:

Delete "$INSTDIR\boot.ini"
Delete "$INSTDIR\manifest.dat"