[Help] Modding PS2 Games

So the modding of PS2 Games seems to be harder than PS3 games cause there are more security checks on the ps2s Game ".ISOs" compared to the PS3 games which are in a simple folder.

TOC* Checks the size of all the files in the .ISO. If any files are modifyed they dont match the TOC and the ISO will be corrupted
LBA* Checks the order of the files. In which order they are inside the ISO and if any file is missing (dummy-files for example) If the order is incorrect/changed or any file is missing we will get a Corrupt ISO once again.

So the problem is: How to rebuild the ISO after modding the files.

The LBA shouldnt be a problem in most of the cases cause usually you dony have to delete or ad any new files in the ISO, only replace or edit the existing ones and some/most of the "ISO Creating/Burning/Extracting" Softwares have the option to choose the order of the files while creating the ISO-Image.
And some software rebuilds the TOC correctly

But all this is a big pain in the ***... (Searching which software can do both of the things, adding all files manually)


So i heard about this little app "PS2 Xpert by Gnie" Which should do all that progress automatically and i followed these instructions:

to rebuild the iso (fake TOC) with the files in the same LBA order
Step 1. select the iso.
Step 2. click Extract LBA (auto sort lba)
Step 3. click Extract File
--Now Mod The Extracted Files---
Step 4. click Rebuild File
Step 5. click Rebuild LBA

But for some reason the game still isnt working it now crashes after the PS2 Logo in the first intro.
The mods work ok, the problem is just that the game doesnt boot at all, but i can use my original/not-modded game to get past the booting and then swap it with the modded disc and then the game works fine and the mods work fine also.

So is there some kind of a check at the start-up of PS2 Games or what is the problem???
They have Checksums/ Hash???