hi,
first of all, you should understand that those datasheets and the Flip are different Atmel products (= Now, ask yourself: what does mean BLJB? Boot Loader Jump Bit, yeah? Now we look at Flip software and have found that this bit is set. What does it mean, again? Yep! It means: go to bootloader! Please understand that datasheet describes exactly-internal-hardware state of this bit; opposite to Flip which shows you real used-accepted flags. Why are they not the same? Oops, ask Atmel then.
Another way. When you have soldered non-programmed chip and then run Flip and connected to it via Filp - what do you see? Yes, you see the checkmark on BLJB. So what does it mean? Exactly! a chip has not been programmed yet and so it stays at "ready-for-bootloading" state. Just load program into it, then clear BLJB, Save chip configuration`s bits into it and okay-dokay! Switch power on/off - it starts to your program IF there is no hardware conditions detected.
I can try to reset the bit, but im afraid of getting no connection to the controller once i've reset the bit.
Arhm... Sorry, it seems you do not understand the basis fact of matter: you will not be able to start internal program at stand-alone mode (without Flip) as long as you either not clear this bit or put OWN boot-loader vector at least.
The main way: download program to a chip via Flip, clear BLJB there, set needed protection bits and switch off/on a board. If your program has a chance to fault then ask schematic engineer to implement a switch which provides hardware bootloader conditions (as for me, so I always have this back-drop way implemented :)

cu!