I just get the feeling I am missing something, but what I am overlooking, it eludes me.

Rundown:
I have 32 Par 38's. I have them on 4 T-bars, 4 on top, 4 on bottom. I gel them R,G,B, Yellow on top and in the opposite order on the bottom. This ends up giving me a right side of all 4 colors and the left side of all 4 colors. I then aim the left side to one target zone and the other side to another target zone. I control them via 1 dimmer pack per tree. Each tree uses it's own 4 addresses. I am therefore using 16 DMX channels to properly run 32 lights. Nothing absolutely out of the ordinary except maybe the number of par 38's.

So, I have added the lights in MyDMX, using channels 17-32. Again, no problem.

I've gone into the 3D Visualizer and NO, I am not looking for a profile to represent a dimmer pack!! I have properly colored those fixtures in the 3D Visualizer in the fixtures tab.

Again, in the fixtures tab, I select the lights I want to duplicate. I work in groups of 4, so we'll use channels 17-20 for now just to keep things simple. I duplicate them, I set the Y offset to .5 and the duplicate lights appear ABOVE the original lights. Of course, the lights are not in the position I want them to be, I fool with the matrix and get that resolved. Of course, now I have to go through the painful process of moving these to where they all need to go, but that goes well, all things considered.

I'm working on my "default stage".

I save often. To the point of paranoia.

I QUIT the 3D visualier and when I come back. I get an notice that things have changed
WARNING: patch has changed!! automatic mode.

My new lights are GONE.

I do it again, same results.

I try again using my follow spots because they are easier to select, and same deal. I do this in the listing window under the Fixtures tab. I then g back to USER mode and save. I quit the 3D Visualier, and when I re-enter, I see the spots BRIEFLY before they vanish and I get that error again.

I do this via the "add fixtures" and it does the same thing.

Now, the option to buy more dimmer packs simply isn't in the budget. Buying more lights isn't in the budget either.

While frustrating, this isn't a killer, but it it is annoying and should be investigated.

Or, do I need to redo these lights in my Universe because I've done something wrong there?

I'm guessing you got this fixed, but for the sake of anyone else that runs into this problem, this was my solution.
Once I had all of my fixtures built in the visualizer, I saved the stage outside of the program and saved a copy to another location as well. This has saved me a lot of headaches in rebuilding this show so many times during the learning process...
As for needing extra channels, I doubled the channels for visualization purposes, saved the show, then deleted them to save the final product. As long as everything is symmetrical, it has no effect in the final show. Saving multiple shows in multiple areas may seem redundant, but it's help in the long run and forced me to create backups for everything.