Trouble with transparency - help!

I just got started designing textures and I've been going crazy with transparent effects applied to simple prims. At first I noticed a few glitches when using my objects but it seemed livable. Then I thought of a new project -- a cabin shaped like a lotus blossom with only 2 prims. When I applied the texture, it came out translucent. Not just the transparent parts, but the whole thing. I'm sure I didn't put partial transparency there. Together with other odd glitches, it looks terrible! Then I tried making a non-transparent version of the same texture, and it displays fine, but doesn't have the jaggedy effect at the top that I wanted.

I can't tell if it's a bug or if I'm doing something wrong. Any advice appreciated.

A picure of the cabin.
In addition to the translucency, there's an odd glitch at the bottom where it interacts with the lily pad (which also contains a transparent section)

The cabin with a solid texture
The cabin looks better, but now part of the wings are cut out by the lily pad. Both wings and lily pad have textures with transparent sections.

Does anyone know what I am doing wrong? Or have you seen any graphical glitches when using custom textures with transparent panels?

Well, there's good news and bad news. The good news is you're not doing anything wrong. The bad news is the problem is systemic, not somthing you can fix. The phenomenon, known as alpha sorting, is an issue with the way SL (and a lot of other games and 3D modeling applications) utilizes OpenGL. It is very common.

What happens is when two surfaces with alpha textures (alpha meaning transparency) overlap in close proximity, the renderer has trouble determining in what order to draw them. Most commonly what it ends up doing is drawing the one that is most perpendicular to the camera, and then not drawing the other one at all. Sometimes it may draw part or all of both, producing a translucent effect like in your first snapshot.

The upside is that objects like fire, bushes, trees, etc. can be built to take advantage of the "glitch" with nice effects. The downside is that other objects, like the one you're trying to make, are pretty much impossible. There are of course work-arounds, but they are extremely prim-heavy.

Thank you, Chosen.

It's also good news that I don't have to spend any more time trying to fix this!