Well, the first obvious thing that comes to mind (and knowing you've had corrupt preferences before) would be to try resetting the preferences via the preferences dialog.
Edit: I've found the error, and I'll detail more info in a bit as I'm just getting it into a presentable format...
Okay, so first things first - to get your tools back to how they should be:

- SEVEN.png (115.98 KiB) Viewed 4669 times
Immediately after doing that, quit OXT Lite.
Reopen, and the tools should be back to this:

- EIGHT.png (85.26 KiB) Viewed 4669 times
Why did that happen? Two reasons:
The first reason is that I thought I'd covered every possible combination of hiding/showing sections, but I was missing three if statements. I've added those in this replacement revTools stack, so please replace that to banish this error and stop it happening again: (Thank you for finding it by the way)
Secondly: The popup menu for hiding/showing these sections seems to work when it feels like it (and this was a bug that was seemingly always there - it starts to get unreliable upon hiding / showing 'Graphics objects' and 'Graphics Tools', so this will be one for me to fix. (Again, thanks for finding that). (Sometimes it seems you have to toggle 'Graphics Objects' first before you can toggle 'Graphics Tools').

- TWELVE.png (347.76 KiB) Viewed 4669 times
I had to use the following message box commands to reliably hide/show sections in the end to not have to use that menu:

- TWO-mb.png (30.5 KiB) Viewed 4669 times
With those steps done (resetting the prefs via the dialog), quitting and replacing that revTools.livecodescript stack, I can confirm that this should indeed work and did the following test:

- tools-all.png (304 KiB) Viewed 4668 times
I still wouldn't use that menu to hide and show sections, but if you do - be aware you might have to show / hide them multiple times to actually get the sections you want to appear in seemingly random orders. (I will fix that too, as I mention above - but didn't know about that) - so putting my three if statements in resolves this until I get a chance to reliably fix that menu.
edit 2: Just checked out of curiosity and can confirm this weird behaviour of showing/hiding sections via this menu is present in LCC 9.6.3. Obviously the OXT lite section headers aren't there in 9.6.3, so it doesn't get itself into such a twist. It's just that you are telling the tools palette to hide a section, the menu is broken, but then the section shouldn't exist - so the problem is exacerbated when my section names try to populate. Short version: if I fix the menu bug which came over from LCC 9.6.3, it'll ensure that we don't get any weird behaviour like the above again.