[vbat99]

I've got some "issues" which are probably created by me and not the fault of the program.  I change movies.... a lot.  What I mean is that I will have a Web-DL copy and then I'll "buy" a BluRay copy and then either a 4K or a REMUX.  The program gets all sorts of messed up since I'm constantly changing the quality of the video file. 

I do this all the time. Are you keeping the older quality videos as well? If not, what I do is copy the new, better quality movie to the existing movies folder.
Delete the earlier version movie (movie only not nfo, artwork etc).
Then rename the new version to match the nfo filename.
In MC, find the movie, and right click it.
Select Rescrape Specific -> Media Tags
This will update the nfo with the stream details for the new video file.
done!

I have about 4 duplicate entries for certain movies in the list.  I've tried to remove the movie folders that I have set up to scan, thinking it would clear the cache and then re-add the movie folders, but the same issue presents itself, duplicate entries.  I will highlight all the duplicates, select "rescrape all" the duplicates will disappear but will re-appear on the next loading of the program.  
I've also have movies that are listed, that have been "changed" and the entries are blank as well.  No matter what I do, I can't get them to show up in the program.  Trying to rescrape these missing movies will result in an application crash.  Trying to open the folder from within the program results in an application crash, etc..etc.

Looks to me like you might need to start from fresh.
I would delete all nfo's (nfo's only, not the artwork or actors (why download them again))
Do a Refresh All in MC.
Then do a Search for new Movies

Also, where in the heck is the option to disable the movies from being put into collection folders?  I thought I had found that particular option (I don't want collection folders) but a rescrape caused movies to be placed into collection folders again... lol

Look at Movie Preferences -> Renaming tab.
The folder renaming %N\%T (%Y)
Just remove the %N\ and a collection folder will not be created when the movie is renamed.

BTW, I do recommend not using IMDb scraper. Select TMDb Scraper and pick the IMDb items you want from IMDb.
ALSO. Disable Auto rename of Files and Folders during scraping many movies.
Why? Just in case they are scraped as the wrong movie, you do not what to have to hunt for missing movie's if they have been renamed.

Good Luck.