I am wondering if this is an issue with the MBR (Master boot Record). I am looking and I know there is a FIXMBR command, but I don't know where to use it or the syntax....
If you want to look into this, read this thread all the way through, but use caution. Ask for advice first if you want to try this route:
How to fix MBR through command prompt?
Don't do any of the commands unless you have everything backed up. messing with the MBR can mess things up worse.