When I right clicked on the swf file, I was given all the options for applications that would open the file. That is when I discovered that somehow my default application to open the swf files was changed to a projector I had made in Flash. (A projector is an application you create to allow the swf to play on anyone elses computer even if they do not have Flash.) The projector was originally made for that 2.0 file, that is why it kept opening the 2.0 file on top of every new swf I made.

All I had to do to solve the problem, was to find the projector on my computer and delete it. Then everything reverted back to the correct default application and all the overlapping stopped. (If I did not want to delete the projector, I found that I could still eliminate the overlap by right clicking on the swf and choosing the correct application to open it. Since I did not need the projector anymore--I decided to delete it.)

So that is the end of the mystery!
Hope the information is helpful to someone else in the future.