So not sure if I'm alone here or if this is a coincidence but recently I have had this same exact issue on two completely different systems (once acer laptop and one gateway laptop) with the only common denominator being Windows 7 Home 64-bit as far as I know...
Basically I would run my routine HitMan Pro scan and in the instance of these two laptops HitMan would need to reboot in order remove the remaining trojans. Well, after the reboot the system will only boot straight into the manufactures recovery partition.
Interestingly when booting from the Windows 7 disc and navigate to "repair" it doesn't even detect an existing operating system.
So not sure if there is any simple MBR fix I could do or even what direction I need to be looking for a solution, any input is greatly appreciated, thanks :)