Firstly, I'm a MO user. Well, I've just updated SKSE. Seemed quite easy. I just double clicked on the program and it automatically found the SKSE folder and installed itself. Simple! But then I tried to update SkyUI and I got this message:

This report informs you about potential problems with your SkyUI installation.

Fix these problems , then press 'Refresh' to confirm that they're gone.
After all problems have been resolved, you can continue with the installation.

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Problem #1:
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The Skyrim Script Extender (SKSE) is not installed.

Solution:
1. Get the latest SKSE version from 'http://skse.silverlock.org/' and install it.
If you have problems installing it, have a look at this video:
http://www.youtube.com/watch?v=xTGnQIiNVqA

But I just installed SKSE! So, I installed SKSE again and tried, once more, to install SkyUI. Same message. Any idea what's up, why SkyUI doesn't know I've got SKSE installed?

Make sure you're running Skyrim from skse_loader.exe in your Skyrim main folder. If it's not there, you didn't install it correctly. I recommend the manual installation over the installer.

Yep, checked the Skyrim folder. I've got:

skse_1_9_32.dll

skse_docs

skse_loader

skse_papyrus_docs

skse_readme

skse_steam_loader.dll

skse_whatsnew

It might have something to do with this, if you have Avast Antivirus. - http://www.reddit.com/r/skyrim/comments/1pbira/psa_for_pc_users_of_skse_and_avast_antivirus/

Nope, I have AVG. Also, rather than making a new thread I've got another question. I just a few minutes ago updated MO. After updating it MO told me I was missing something called "Python"??? Never heard of it and it doesn't explain exactly what it is in the linked page. Maybe someone can fill me in?

See the FAQ section in the MO description:

"Q: SkyUI (or some other mod) installer says SKSE is not installed although it is!
A: Due to the way MO works the installer can't see SKSE. If the installer allows you to continue despite the error (SkyUI does), do that and the mod will work. If the installer doesn't you have to use a different installation mechanism (i.e. a manual installer)."

The fact you have all the required files except the skse_loader.exe suggests to me that regardless of which antivirus you use, this is essentially the problem you're having. I mean, it could be something else... but there's a very high likelihood it's an AV issue. It's also not strange for something that one AV program flags to start showing up as flagged in other programs in short order even if it was a false flag. I'd check your antivirus' quarantine and set an exception for skse_loader.exe, then try to install it again and see what happens.

Basically, the reason why I was trying to update everything is because I'd just installed "A Matter of Time" and it wasn't showing up in my Mod Configuration menu. It was showing up on screen, but it wasn't registering in the Mod Config options. I looked on Nexus and it said I needed everything up to date or else it wouldn't work properly. Now, after lots of sweating I've updated everything, even MO! When I tried to reinstall SkyUI, sure enough, it said I didn't have SKSE, but I went ahead and installed it all the same, thinking it might be what schlangster said. Yep, the game booted up a-okay. And yep, most of my mods were showing up on the Mod Config menu. But damn, A Matter of Time still wasn't there! So, I walked around for a few minutes, then tried the Mod Config menu once more. BINGO! A Matter of Time was there in my menu! Everything seems to be working alright too. *Breaths a huge sigh of relief*

How strange. I've just done a BOSS scan. It says SkyUI should be high up right above IHUD, but when I return to MO it's still right at the bottom of the load order. For some reason it's not moving SkyUI when BOSS tells it to.

I'm not sure what "MO" is, but you can just manually move it up your load order.

http://skyrim.nexusmods.com/mods/1334/?

You need to run BOSS inside MO in order for it to affect MO's load order.

Yep, I always do. I've got everything running through MO. I've now found that my new version of MO doesn't move any mods after a BOSS scan, I have to move them all myself. I don't know if this is something new or if there's something wrong, but my new MO does have a handy new feature. Before it was a bit of a hassle to force a change in my load order against BOSS, but the latest version of MO allows you to simply drag and drop the specific mod and then "lock" it in place.

this.

actually, any program (tes5edit, wrye bash, skyproc patchers, etc...) should be launched from Mod Organizer. MO launches programs in such a way that the program will think your Data folder is actually the merged version of your Skyrim/Data, MO/Mods and MO/Overwrite folders. If you do not launch from MO, the program will think the data folder is empty, because it is.

you can very easily set up programs to launch from MO: in the select box next to the "run" button if you choose edit it opens a screen where you have to select the executable, and then you can select the application from the select box and click run and MO will do its magic

edit: i see you already know this...