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How do you have 2 Master HDD's? That doesn't work. Is one SATA and one IDE you meant?
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there are two IDE channels, each can have a master drive: Primary Master and Secondary Master.
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If it is the second problem you will have to boot a liveCD and edit the file /boot/grub/menu.lst . There are a number of different things that could cause this problem, but two causes that I can think of would be a zero second timeout before selecting the default option or a hiddenmenu option. Reinstalling Ubuntu will get you a default menu.lst as well.
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this sounds the way to go. if it doesn't work it could be that the boot flag in your partition table editor is against your windows partition (no idea why this would have changed itself) and it could be changed to the partition with GRUB/LiLo installed with a partition editor.