When you boot the Ubuntu installation medium and select "Try Ubuntu" and get to the Desktop and click Install Ubuntu, you will have several options. Install Alongside may be there, Erase Disk will sure be there but if you have and want to keep windows you don't want this. There should also always be the option "Something Else" which is basically a manual install. Select that and you should get a windows "Allocate Drive Space" and your hard drives and partitions should show in the main window. If you don't see anything there, do not proceed but post back and indicate what exactly happened and any messages you may have seen on screen.
Quote:
partition 1 does`t start on physical sector boundary
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Seeing that in fdisk output is usually not a real problem. If that is all you see, it is definitely a problem. You should also see the drive and partition information. If you get that post it here for help.