Prims showing through other prims

[Rdy2Go]

I am using firestorm viewer.

Recently the water that is in my skybox(blue green strip) has started showing through my window/door textures. It does this with multiple buildings so I have ruled that out as an issue. Just hoping it can be fixed, image attached.

[Rolig Loon]

That looks like an alpha conflict.  Since both the window and the water prim have 32-bit textures on them, your graphics card can't figure out which one of them is "in front" of the other, so they both appear.  It's expected behavior, and not peculiar to SL.  It's a "feature" of OpenGL applications.  The way to beat it in this case is to replace the texture on the window with a 24-bit version of the same texture, so that it does not have an alpha channel.  To be clear, it doesn't matter whether the window glass is transparent or not (and in this case, you don't need transparency anyway).  What matters is that its texture currently appears to have an alpha channel and hence the potential for transparency.