It's not the tools you use, but what you do with them that counts. Take a look at my two most recent skins Styl and tell me you can't get a 3D look with gradients. I don't even use Photoshop...
Regarding your '3D' skin, I agree with Hippy & co. What you've produced could easily be replicated in Photoshop using simple gradients, bevels and drop shadows. The bottom part of the Start menu is just a vertically-flipped copy of the top. If you want it to look like your light source is in front of the skin, the highlights and lowlights should be consistent over all curved or rasied surfaces. At a stretch, you could say that your Start menu is lit by two light sources, both positioned at the very top and bottom edges, with the curved sections being raised enough that they cast the opposite ends of the menu in shadow.
I hate to say it, but Hippy's quick attempt with gradients actually looks a lot more '3D' than yours anyway. I think you just need to look a little harder at the skin library here to see that 3D-effect skins are what WindowBlinds does best. Compare the skins here with the multitude of flat 'minimalist' styles available for that 'other' skinning engine (

) and you'll start to realise we're actually pretty well off already.