Very nice looking! I haven't d/l it yet, but I can offer a few guesses on what the problem would be.
It seems like what this does is replace the textures for the drop particles used in smoke effects. Normally they are sorta these amorphous blobs of grey/yellow; these new ones look like they were lifted from actual photographs.
The 'blinking' most likely comes from the particles being dropped too quickly. Unlike the old amorphous blob particles, it would be really noticable when one of these detailed particles suddenly jumps in front of another one.
The solution might be to change the sections of the game's config.cpp that controls how the particles are dropped. Exactly which section this is, how it works, and what to change is beyond my knowledge, but conversion mods like the ECP, FFUR, FDF usually change this stuff, so somebody out there knows how
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