I have made some carrots, and used a transparency mask for the leaves.
When placing them on the magisplay, the ones at the back and the front right ones appear under the tray, the other ones at the front correctly show on top.
How do I solve this?
Thanks!

Did you use "blend" in the "stdMatAlphaBlendMode" in the TXMT? Try with "None" and also change the “stdMatAlphaTestEnabled” from 0 to 1. These settings work best for cutout-type objects, basically anything with greenery.

The Blend/0 settings work best for actual transparency - things that are see-through, like glass. It usually doesn't work well with non-transparent textures (often causes them to "invert" so you kind of see the inside of the mesh from some angles).

The Magisplay tray most likely has the Blend setting since it is transparent, and may be causing some weirdness with other meshes with the Blend setting and/or transparency in general.

That was it!! Thank you!

Although I am having related problems with my drink bottles. It doesn't matter what I set those values to, they always look like this: (the bottles behind jump to the front)

Can you upload one of the soda files? I have a couple things I'd like to test out if it works, but I'm not entirely sure if it works in your case. Transparent objects can be a pain...

Have a beer!

Texture - Import as DXT5, it works better for transparency. Can also to some extent reduce the Blend issues.

Sometimes it helps to have each individual item in the mesh as its own group (you can have several with the same name in the mesh/GMDC, it's useful for anything that's transparent or layered but needs just one set of textures). I tried that with the file below, see if that works in your game. I only did some basic testing in Milkshape with the alpha settings. I added the Milkshape file so you can see how I did it (comments editing of the opacity settings + exported/imported as Unimesh, but remember to copy/paste the GMDC filename). It looked fine for two of the settings - the last one tend to look a bit borked anyway. You can experiment with the opacity settings. It's possible it could work to have all of them as -1 or 1.

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Shadow - Should be 512x512/256x256/128x128 or similar (or 128x256, or any other variant of the "power of 2" sizes), regardless of whether it's hidden or not. The 350x567 size could cause potential issues, at least if you ever add a shadow of that size. I don't think that's what's causing your current issues, though. To fix, import a texture of the proper format as DXT3 and change to the ExtRaw8Bit format before commiting.

Thanks for taking a look!
I managed to change the shadow format (I only used the other one because that's the size it was in the original Maxis file) but not sure what you mean by " change to the ExtRaw8Bit format" - where do I do that?
I also can't work out how to import the bottles as individual items into the GMDC??
Are the opacity settings the stdMatAlphaMultiplier value?
Anyway the result is this: bizarrely, from one angle they are still wrong, from the opposite side, they are fine...

"change to the ExtRaw8Bit format" - there's a dropdown list to the left in the TXTR, where it says DXT3 or DXT5 when you've imported. It has ExtRaw8bit as an option.

I saw the same tendencies in Milkshape. I often use it to test whether opacity will work or not ingame, and it's surprisinglly accurate.
It has three opacity settings (import the mesh and add the texture/material, right-click the 3D window, find "Transparency", and there's "Simple", "Alpha Buffered" and "Alpha sorted". The two alpha ones look fine, but the "Simple" one has the same issues you see ingame.

The issue seems to be that the game doesn't quite know which item it's supposed to prioritize putting in the front and in the back (it's one of the issues with the Blend setting). I tried to "trick" it by changing the order of the bottles, so it looked fine from the front, but it still had the side issues in Milkshape. It is possible the only way around this is to make single bottles.

You can use the Unimesh import/export for layered meshes like this (same import/export as for clothes). In SimPE you replace the mesh by right-clicking the GMDC and choosing "replace" (but copy the "filename" first, so you can paste it in before commiting).

I managed to import the single bottles in the manner you instructed above! But there is no improvement, unless I missed a step. They looked fine in milkshape (except under "Simple" transparency settings, as you said) but the game still can't display properly.
I think maybe I will have to abandon transparency and just make them shiny??

That's one option.
You can also try with just one bottle in the mesh, and see if you get the same issues then when you place multiple ones next to each other. It's usually when you have multiple items in the same mesh you get these issues with transparency.

I started out with one bottle, but I want a bunch of them for my supermarket.
The annoying thing is that they show up wonderfully in SimPE but the game can't cope.