Everyone, thanks for the support.
Rich, I have since reformatted the hard drive with different boot codes. However I did save the file /mnt/sda1/tce/boot/extlinux/extlinux.conf which was:
DEFAULT core
LABEL core
KERNEL /tce/boot/vmlinuz
INITRD /tce/boot/core.gz
APPEND quiet waitusb=5 norestore waitusb=5:UUID="387ce92a-7c48-4129-a30e-eeb6de6257c0" tce=UUID="387ce92a-7c48-4129-a30e-eeb6de6257c0"
Yes, I know waitusb=5 is duplicated. I don't know why.
At this point, I have decided just not to update the extensions that I think are causing the problem so I can move on and start configuring the computer for my use. Like, I have emojis working now...
Once I am done making my own remaster, I might go back and try to recreate this issue. Until then I probably won't be able to respond to any posts (at least not quickly - I will probably create new thread with concise info later), but again thanks for the help so far. To me the biggest hint was the error caused during boot, "ln: /usr/share/X11/locale No such file or directory." Also, my Core Plus 9.0 image iso is from March, if that matters? Another weird thing that was happening originally, was that there were duplicate instances of flwm_topside on the onboot list. I'm not sure what caused that.
A summary is: I had Core Plus 9.0 installed to a hard drive, with a persistent home. I did not mess with any files manually such as .filetool.lst and .xfiletool.lst. I have boiled the problem down to, I install Core Plus to hard drive using the GUI from a CD, and when I update the apps through GUI, (list posted previously), my background logo disappears and I also cannot set the background to an image. A workaround (for me) was to re-install Tiny Core from CD to hard drive, without reformatting the hard drive. This brought the logo back and the ability to set an image as a background. However I started completely over and reformatted the hard drive again to be safe.
4) So if you like no persistence....as you booting with norestore....IMHO your Original Post where you thought you made gtk3 onboot and other stuff....they should not have persisted....and you will be forced to download and load them each and every boot.
And TC has invented Ondemand....which might be what you are looking for?
but as time goes on....why not have a tce dir as a persistent dir to save those downloads?
is that clearer?
Thanks aus9. I first had a persistent home when the issue started. I then removed persistence (through the norestore boot code, I did not change any /opt files), but the issue was replicated (which makes me think it is a problem/incompatibility with the extensions). With experimentation, I am better understanding the benefits of Ondemand and I am using it more. I also agree with your explanation of norestore, and I am using it for boot up / shutdown speed and cleanliness.