After 5-10 minutes of the game - the texture disappears. Moreover texture "transparent" repeats grass texture in the game. All dependencies identified and verified several times. What else can you do?
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That's the transparent base texture bug. I think it happens when you go into underground view, IIRC.
IF all the textures are installed, then you cannot avoid this issue. Lots simply can not show transparency without special tricks. I.e. making the base a prop and not a texture. So if you have an overlay texture on a lot, without a base texture, then this bug will appear.
Simply turn the Zones data view on, then off again, the problem will go away. This is only temporary though, certain actions, including entering the water/underground views and saving, will bring it back once more.
The permanent solution is to install the missing base textures, or to add them using the Lot Editor if none existed to start with. Some people prefer to live with this and have transparency, but personally I prefer not to use such lots.