This is either a graphics card problem (hardware limitation or driver problem), or something related to your saving method of the in-game graphics.
What MediaVP's are you using?
If the problem happens with current, up-to-date MediaVP's, then it's probably a GPU/driver problem, in which case I ask you to tell us what GPU are you using, and with what drivers? Could you also post your fs2_open.log, that should tell us if something in OpenGL initialization fails.
If it's a data problem instead, here's what could
possibly cause it on incorrectly saved textures:
Green is only used for 1-bit alpha on specific type of PCX files. You shouldn't use it for any other type of files. Most effects should use additive blending, which is achieved by making a 24-bit RGB texture with black background and no alpha channel
at all. If a texture that is supposed to use additive blending happens to include an alpha channel, that can cause effects that you have described, since the game things it's supposed to use alpha blending for that effect and the alpha channel happens to be fully white - which will create an opaque black box around the effect.
If that is the case, you'll need to look into the settings of the program you are using to save the images, and make sure you eliminate the alpha channel where it is not needed.
But, if the problem happens on all mods (most useful test mod would be mediaVP's, because we know they should definitely work correctly
), then it isn't a data problem.