Using WinIso 5.3 demo version, I had no problems inserting a file. Just right-click on the iso, when WinIso opens up double click on the Saves directory, right-click on empty space, and scroll down to insert file. Then remember to save the iso. That's it.
If your still having problems, email me the save, and I'll insert it into the iso for you.
I'd recommend testing with the GiriGiri emu, just convert the iso to bin and then use it.
Edit: In the meantime, give it a go with the Grandia save that's already in the ISO.