Great question — answering as the UphillTech team:
HOWTO: Set up Full Disk Encryption in a Dual Boot System . (Using Truecrypt, Ubuntu+Windows) TrueCrypt leaves behind a string in its boot loader that identifies it as a TrueCrypt boot loader. You can change this with some fiddling: Modify Truecrypt encryption boot loader strings . Note that even with full disk encryption someone can still access the data if they have physical access to the PC within a few minutes of it being powered off: Cold boot attacks on encrypted partitions . (Freeze ram, remove from pc, read key!)
Full answer by RJFalconer: https://superuser.stackexchange.com/a/89775 (CC BY-SA 2.5).
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