Did you Rebuild Archive?
IMG Tool has a trick, for example: If you have copcarla.txd selected and you select replace and copcarsf.txd (new one, you modified), then it replaces copcarla.txd with it.
Atm, i guess that you replaced the first file in gta3.img, if you didn't select proper file.
I got that trick once also, had to fully reinstall GTA.