First thank you for your help sATCx.
I am not sure why windows made the boot.ini like this, but you can modify this by right clicking on My Computer/Advanced/Startup and Recovery Settings, or by editing the ini file. What should be there is timeout=0 or in the settings window uncheck 'Time to display list of OS'.
BOAC is correct, it has nothing to do with partitions. What I did was boot into recovery console from the XP CD, renamed the first installation of windows (could not do a rmdir or and equivalent to delete it), installed another windows, then deleted the first one. What I was concerned about was the Master Boot Record, I suspected it would have 2 OS in it (not sure if this is technichally correct, and maybe someone more knowledgeable can shed some light).
Hopefully the title and content of the thread are more accurate than the post referenced to goates, which will make the search more obvious
