With FS9 models, transparencies by material should be at the bottom of the parts list in the modelling hierarchy, ie. last. If they are not, other parts appear in front of them. This is an issue in FS9 also, just not noticed by many people, you need to look closely to try and see a difference between, say, the wing that is behind and not behind the canopy glass. I'mnot sure how incorrectly ordered parts would manifest in FSX, but may result in parts becoming invisible? Fix would be from source or backwards engineering through MdlConX or possibly SCASM/hex editing.
If you have a prop disc that is fully opaque and uses textures for transparency, to find out, rename the texture folder sothe model shows 'naked' in sim, ie. base materials show. with engines started you'll see if the disc is opaque. If it is there may be a fix. This ultimately depends on if the solid disc uses it's own material or shares a material with other parts. If you want to make it transparent, you don't want other parts affected, transparent wings, etc.
The way I know of is to use mdlMat by Martin Wright, ACM (or other model viewer that allows different anim states) and notepad (or paper & pen). Using mdlmat you can change colour and transparency of each material in turn in the model (FS9), say to solid bright pink (as it is very seldom used by modellers), load the bare solid model in ACM, look for pink bits, revert them back to original properties (hence notepad) then move on to the next material, so on and so forth, until you find your solid disc, if it is then the only part solid pink, your in luck, revert the colour, add transparency and bingo. If other parts are affected, your only choice is backwards engineering, sorry.
Jamie