I believe I have a problem of great proportions.

[StealthSupreme]

99%.

I, this morning, spent exactly 6 hours and 30 minutes completing the SSE, from SCRATCH, after having deleted all of my Brawl data (for this very reason).

With my laptop next to me I followed an FAQ, which detailed where each Orange Box was and how to obtain it...

But it would seem that ONE of those Boxes has escaped my grasp...

I realized this when I completed both parts of the Subspace Bomb Factory, where one is supposed to have 64% completion at that point. Alas, I only had 63%.

My question is this: Is there any way I can identify where exactly this last Orange Box is, so I can unlock Boss Battles...finally...?

 

[Ixnay]

It's gotta be in the one stage with the green flag on the map screen, since if you have 99%, all of the other stages should have the flashing marks on them. I'd search that stage using the FAQ, leaving no stone unturned, and if you still can't find the last box, then I would assume the FAQ is incomplete. Hope you get your last 1%!

 

[Abramovici]

My question is this: Is there any way I can identify where exactly this last Orange Box is, so I can unlock Boss Battles...finally...?

I'm pretty sure you don't need to get 100% to unlock boss battles. Have you Finished Tabuu? If not, you won't unlock boss battles and won't get 100%

 

[nugget]

omfg im missing 1% in the bomb factory too!!! (might even be the same level)

ive gone through it like 20 or so times and i just cant seem to find that last orange box!

it's really crippling...

 

[Rew]

It's not always an orange box that you need to get 100%. Sometimes there are trophies that are hidden in clever spots that also count toward your percentage.

Anyway, like Ixnay said, look for the one stage that still has the green flag, then look at all the walkthroughs on that particular stage (in case the one you were using has failed you), and get to it!

 

[Tangy]

http://guides.ign.com/guides/748545/page_166.html
This is a guide that shows each orange box and each trophy laying on the ground. I double checked through it, in case they might have missed something, but they got everything.

 

[RickyFLDMS]

I had that problem too, the hidden box in the factory. Start from the beginning and enter the first door on the wheel platform. There should be five springs in that room; 2 on the left, 2 on the right, and one spring near the top of the room that looks insignificant. Jump on that spring and attack the air when you're off-screen.

Hope that helps.