I ran into this issue before many moons ago.
I have no idea why my system at the time was not booting to CD.
It was the same situation you are having but was quite a long time ago on an older system.
I do remember what I did to fix "my issue".
I booted into a Linux command prompt.
Than I did
or most likely
for your hard drive.
Than press m for options.
P to list all of your partitions. You will see your linux system there.
D to delete partitions.... than D 1 for partition 1 etc...
W to write the changes...
E to exit
You should have a fresh hard drive to start your installation of windows now.
And your machine can not possibly boot to Linux as it is no longer there.
I used this and it worked for me. I keep a Knopix CD on hand to get me into a command prompt for emergency problems if I need it.
Also I would wait as I am sure somebody will chime in with a alternative solution and they may say I'm crazy.
I never have found out why this happens. I just removed the problem. The linux boot partition.