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It could be a couple of things. You need to make sure you extract images from the TXD files as 'PNG' format images, because PNG support 'alpha' or transparency, whereas others do not. If you have been doing this, you need to make sure that the image editor you are using supports transparency. Microsoft paint would be an example of this. More advanced image editors like Photoshop and the gimp will, however.

You need a tool like IMGtool, all you have to do is open up the file 'GTA3.img' in the 'models' folder of your San Andreas install directory using IMGtool. From there extract the following files. -tags_lavagos.txd -tags_latemple.txd -tags_laseville.txd -tags_larollin.txd -tags_larifa.txd -tags_lakilo.txd -tags_lafront.txd -tags_laazteca.txd -tags_lalae.txd Once you have these files in a safe place, download txdworkshop, open up each of these files individually in txd workshop and select 'export > to PNG' and save them somewhere safe. Then you can edit the PNG in your favourite image editing software, I use Photoshop, alternatives include GIMP. When you;re done editing, save the file back in the same format and place to overwrite the file, which will probably be called 'grove' or similar. Then use txd workshop to 'import' the edited image into the txd. Once you have your new txd with the logo you want, import it into the GTA3img file using IMGtool's 'add' command. After you have done this for all of the tags, save and rebuild the GTA3.img file and enjoy.