Its a bit late for thiis thread, but I thought I'd also add my experience with aircraft I've built myself. The props are from a template I made when the first aircraft was being made (DA42 Twinstar) and they have transparency set in the model for the prop_slow and prop_blurred prop-disks, and the prop texture uses transparency too (alpha channel).
The odd thing about this is that my aircraft props are compiled using the FS9 SDK and are running in FS9. It seems to be clouds that are darker are more obvious in this effect and the brighter ones would tend to show through the prop better anyway, so the illusion works for that context.
The aircraft I notice it on the most are the Piper Tomahawks for the Liverpool Flying Club, which have alternate red & white high-visibility props. As you can see, the distant clouds are eclipsing the prop, yet in that cloudscape there are thinner patches that the prop shows on top of.
I'm very new to this; my first aircraft was the Twinstar and although I have made another 4 aircraft since, I never noticed the prop problem because I was testing for frame-rates at a remote airport in Libya with 150 parking spots and no weather set.

is the AA5, same prop, same problem, as it will be for the Rockwells (112/4/5) and the ones subsequent to the AA5 - the Jodel and then the Tomahawk. I will probably experiment when I have the time to see whether its my transparency in the model's prop, or the alpha, or the combination of the two that is the problem. I suspect that the problem will be that I have chosen to make the prop disk material (actually two square planes back-to-back, which might also cause the problem (!)) fairly transparent. Since I'm presently running a Twinstar as a flyable plane I will probably experiment on the props after I've refined the wings and fuselage (I'm thinking of a V2 of that model).
I noticed a short time later that the prop sits in front of the clouds until the texture is applied. I was using ctrl-W to switch between AI planes in Spot View and sometimes the textures take a moment to load, especially if you've switched from an AI plane at a heavy scenery airport when I assume the prop texture falls out of the cache. For a fraction of a second the square plane I use to map the texture to, was visible in a ghostly form, then the texture was applied and the prop became round and behind-the-clouds again. I assume from this that I can make all prop transparency built into the model and then apply a solid bitmap on there (eg black disk for a black prop, silver for silver etc). The alpha would then only be used to cut away the square corners of the plane object to give the illusion of a disk, and it wouldn't matter whether the corners were behind the clod since they're not supposed to be there at all anyhow. Of course that might just make the prop disappearance really obvious instead ... if you can see the clouds therough the prop them the alpha was the problem, if it is even more obvious, then the texture would be the problem (because the material untextured shows in front of the clouds as it should). I don't know if that's a good assumption, but from the few clues I have presently, that's the most likely hypothesis.
Assuming I'm right, for planes that don't behave (at least in FS9, which is my sim of choice) someone with experience of hex codes might be able to go into a model and alter the material properties to provide transparency (but then they'd not be able to legitimately re-distribute the model).