Issue when packing bin into MPQ

This is more related to Modding a server rather than running a server but I hope this is an appropriate place to post about this.

Here's pretty much all I went through :
1) I made modification to two Skills in skills.txt and skilldesc.txt and created a new missile type in missiles.txt for the new skills

2) I set my game to launch with -direct -txt and put those 3 text files in the data\global\excel folder in the same directory

3) Launched the game, Every change was applied correctly and nothing major was broken in the process (That I could noticed).
    The modified skills used the new missile type and had correct damage calculation.

4) I packed the 3 bin files created during step 3 inside D2_patch.mpq copied over to my diablo directory and launched the game
     without -direct -txt parameters.

5) Noticed the disaster that just happened. It's like both skills.txt and skilldesc.txt were entirely corrupted, not limited to the two skills I modified. Pretty much all skills from all classes were broken, ranging from Incorrectly displaying/calculating Attack Rating and Damage, using the wrong missile type and some just plain didnt work anymore.

My first reaction was to believe that I messed up packing the bin files into the Mpq. I made sure the files I was using were working when launched in -direct, which they did. Then packed them again and tried it without -direct, same result.

Are some files read differently by the game when launching the game with -direct or -direct -txt param  ?
I just don't know where I messed up.

Im willing to provide more information, screenshots and even the bin files themselves if somebody wants to take a look.
I attached two screenshots, First is when launched in -direct Second is when packed, the bin files werent modified between 1 and 2.