I just tried this and it worked. I created a simple texture in photoshop, made 2 transparent blocks and applied it as a texture and it rendered fine.
The model is green and you can see the green through the areas where i made the image transparent.
One thing you may need to check is if the image is using the alpha channel. If you look at the image in the image editor and make sure the Alpha channel is enabled.
If you want to see the alpha channel itself, select Alpha only in the dropdown list. The alpha channel will show up as a black and white image and the white areas are where the texture will be transparent.
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