KiriKiri game complains about startup.tjs

I've extracted the main .xp3 file from a game, and tried to patch a single line from the script (one that shows up right at the start of the game) to see if I can succesfully re-pack all the files back in and if I can run the game. Besides that line and loslessly optimizing all the .png files (optipng), I haven't done anything to the game.
But there's a certain oddity to the game as it seems to have 3 patch.xp3 files at the root; and the patch2.xp3, parch3.xp3 files contain the same files as in the scenario folder of the main .xp3 file, and most of them are of same size (haven't checked if they have the same content). Could somebody explain me this tangled oddity, and what could I do?

[VDZ]

Can you give the exact error message it gives? Did you edit startup.tjs?

- Here is what it says

I haven't done any modifications to that file. What I modified was one of the .ks files (edited one line in it) and optimized the pngs

Also I forgot to mention that I used xp3tools to both unpack and pack back the files, I haven't tried KiriKiri's original tools because I can't read japanese, and thus wouldn't be able to use it ^^;
I saw in a thread here that sometimes when packing back the xp3, you need to enable encryption, and I don't really know how to do that.

[VDZ]

"Could not find storage startup.tjs" is what the bottom line seems to say. For some reason, it can't find startup.tjs.

It's funny by the fact that the file is indeed there in the unpacked folder, but the executable still complains about it.

[d_fallen_god]

CAN I HAVE THE START.TJS OR THE .XP3 FILE WHICH CONTAINS THE START.TJS OR THE NAME OF THE GAME INSTEAD.

EITHER THOSE 3.

I WANT TO CHECK IT.

Ah, nevermind. I moved start.tjs from patch2.xp3 to the System folder and now it works after I compiled the files again.
Thanks both for the help