I then started working on a new one and uploaded it to take a look at it and, even though I just copied over the old file when I saved, the old image is showing through the transparent background.
This makes absolutely no sense to me.
Now, I did a few things to see what was going on, but had no luck. This is what I have tried so far:
-Create a new logo image, solid color only. I erased some of the image where the old logo was showing up and it still showed through.
-I deleted the logo.png file from the server. Made new logo.png and still had the same issue.
-I renamed the image called in index.php. Same issue.
-Cleared cache and restarted browser
Seems that no matter what I do, this "ghost image" is still there. The only way to get away from it is to use a solid color background.