I tried for around 2 hours with no luck, after i tried to manually swap the files and i got it working after 3-4 tries. Then i realized that the problem was probably in the .bat file so i made a swapper myself and got it working almost everytime i start the game. The thing is with the .bat file you don't really know when the swap is done, in the swapper i made it tells you exactly when it does the swap.
What this swapper do : When you choose Vindictus.exe it does a backup of the FileSystem_Stdio.dll to FileSystem_Stdio.dll.backup in the swapper's folder and saves a config file (Swapper info.vds) with the game executable location, the installation directory and the time (in miliseconds) you choose for the swapper to wait. When you click on 'Swap for edited DLL' it starts the game, and wait for HSUpdate.exe to open and wait for it to close, then it starts counting, then it will tell you when it actually swaps the files. You can still get an error if the time is too short. Now it will detect when vindictus.exe is open and will wait until you close it, then it will swap the original file. There is also a button used to put back the backup in the bin folder so you don't screw your game.
Now the swapper was made with visual basic 6 which is really old but i hate .net programmation so i used this instead and on Windows 7 64bits, so if it is not working on your pc just tell me what error you get, remember to right-click on Vindictus Swapper.exe and choose properties, in the compatibility tab be sure that 'run under administrator' is checked if you are on windows vista or 7.
here is a link to the swapper :
http://rapidshare.com/files/2336995452/VindictusSwapper.rar
Also, you don't have to put these files in Vindictus installation directory, and the hex edited file is already in the rar. If a new edited file is needed just replace the Filesystem_stdio.dll2 in the swapper's directory for the new one.
Edit : FileSystem_Stdio.dat was missing in the rar, and the swapper did not copy this file to the bin folder, i reuploaded it with the file and added a line of code so it copy this file to the bin folder