Ok. There's good news and bad news.
Good News: I got it to work.
Bad News: I still don't know what the cause of the problem was, and I was a little late to work from too much fiddling around.
I started by trying Canadair's suggestion. I did not find any chimney smoke effect. The closest thing I found was coolingtower effect. I removed it and didn't really see any change.
So then I went after the merged/not merged theory. I did a clean install of WOV and patched it up. I then added just the SAM smoke trail effect. It worked pretty much like it should have; nice long visible smoke trails that hung in the air. There was this weired issue with some little smoke puffs shooting out to the side just after launch. It's hard to describe w/o a screen shot. But for the most part everything was alright.
I then added Dueces effects. The problem with the little smoke puffs shooting out at an angle went away, and now I had the nice big launch clouds as well. The SAM smoke trail got noticeably thinner, though.
Then I added the weapons pack. The only change now was that the smoke trail did not hang in the air as long. This resulted in the SAM looking like a "snake" moving through the air. The smoke trail was basically much shorter and the end was "chasing" the missle. Again, a screen shot would have been a good idea, but hopefully you get the point. But for the most part, I'm OK with the end result here: I've got the weapons pack and effects pack, and the SAM's have a somewhat visible (but short) smoke trail to make them easier to identify.
So after all this, I repeated the process with a clean install of WOE. Patched it up and installed the 3 different add-ons in the order listed above. I got the same results. At this point, I was thinking it was going to be a problem caused by the merge.
So I installed WOE again and merged this time. I repeated the add on process. However, everything worked as expected. So it is not a problem with a merged install.
I originally had a couple aircraft added, two add-on terrains, and some different sky tiles installed. It's possible that one of the terrains had some effects that came with it that may have caused the issue. I think both the ANW and Desert I had installed had some factorys that may have used some smoke effects that could have messed it up. But honestly, I don't really need the terrain, and I don't feel like reinstalling if it screws up again, so I'm not going to experiment with that...for now.
The only other thing I could think of, is that this time, when I merged, I merged WOE with a copy of WOV that already had the add-ons installed. I don't think the merge copies effects or weapons, so it shouldn't matter. But it's something I did differently, so I thought I should mention it.
USAFMTL - do you know why installing the weapons pack would result in shorter smoke trails? Is there any easy way to fix that?
Anyways, thanks for the help and suggestions...and for reading this long post if you made it this far. If anyone else has any ideas, they are more than welcome.
Thanks!
Gregg