Theme: "TMNTurtleGuy/ComicBook" (/etc/emulationstation/themes/ComicBook). Same issue in "Arcade" (arcade/theme.xml and mame-libretro/theme.xml are identical).
I think I found it. Edit your mame-libretro/theme.xml file with:sudo nano /etc/emulationstation/themes/ComicBook/mame-libretro/theme.xml
Step 1, line 46:<image name "classic_logo" extra "false">
Change "false" to "true".
Step 2: comment or remove the "marquee" section from lines 60-64. Comment html with <!-- and -->, as in:<!-- <image name "md_marquee"> <pos>0.74 0.086</pos> <maxSize>0.26 0.1</maxSize> <origin>0.5 0.5</origin> </image> -->
With these two changes, save the file and restart EmulationStation; you should be all set!
arcade/theme.xml has a "marquee" section that genesis/theme.xml, for example, lacks. However, commenting out this section, while it did remove the marquee game logo, also removed the system logo from behind it.
In addition, line 46 is set differently between the two. Changing this from "false" to "true" restored the system logo.
I think wheels and marquees are enabled by default, so you need to explicitly make them "false" (not just comment out the "true") in config.ini if you don't want to download them.
You have marquees disabled in the command-line options; however, while that game logo is called "marquee" by EmulationStation, it's the "wheel" art from the scraper that goes here. So if you wanted to disable these logos, you need to disable "wheels" in the scraper instead of "marquees." Then you'll need to purge your cache of the already-downloaded wheel arts.
Of course, this isn't necessary now that you know how to fix the theme, but just for general knowledge.
I appreciate you helping me understand the difference between the marquees and wheel arts. I did what you said there and it fixed it! Thank you!
I've updated my config.ini to not cache marquees and wheelarts for now. Thank you again!