Well, here's a weird one:

It happened to me before, on different characters and on different PCs and I still don't know where it comes from.
Basically, over the course of a playthrough with one character, mods with multiple functionalities will lose some of them.
Sounds a bit weird, so let me give you a few examples:

I start a new character, and I have mods installed like Convenient Horses, Enchanted Arsenal, or Moonlight Tales.
At the beginning of this character's playthrough, everything works just fine: the horses have special keys for quick dismounts, the Enchantments allow customization, the werewolf transformation allow power-jumping and revert form on a press of a bound key, everything's just peachy.

Then, over the course of the playthrough, some/many, but not all of the mods' functionalities will stop working, while the mod itself still is there. The Convenient Horses mod will still allow multiple followers to saddle their own horse, but the key-binding options won't work anymore. The Enchanted Arsenal will still modify the sound of the weapon drawn, but not the visuals of the actual enchantment. The Moonlight Tales mod will still use custom lunar phases, textures etc, but the special key-bound abilities of the werewolf like the power-jump will not work anymore, while things like the post-transformation re-equipper will still work.
And if I start a completely new character, those mods will work again! And then later start to fail again! It's all very confusing...

I use the Nexus Mod Manager, Loot, and I cleaned all the files that had to be cleaned (and I didn't clean those that shouldn't be cleaned), crashes in-game are rare and the load-order itself doesn't seem to be at fault.
I never do anything crazy with mods, and in general I just don't risk mods that might cause compatibility issues, and I don't modify my mod set-up once I start out with a character.
This is all quite confusing to me, and if anyone would have a suggestion as to what might be the problem, I would be very grateful.

Well, as far as I can tell, the Papyrus log seems fine, well, as fine as a papyrus log can be, anyway.
Tried a few debugs, included those provided by the mod authors, none have worked so far.
Also checked the SKSE log, nothing there either.
However, uninstalling the mod, making a new save without it, then re-installing the mod seems to fix the issue temporarily.

I uninstalled the enchanted arsenal mod, saved, quit and loaded the game, re-activated the mod and loaded the game again, and it was working just fine.
I then tried to do the same with Moonlight tales, and the bugs were fixed there as well. However, the enchanted arsenal wasn't working anymore after re-installing Moonlight Tales.
Since the two are unrelated and modify different things, I do not think this is a compatibility problem.
And I'd rather not have to uninstall and re-install a mod every so often.

Is there something specific I should be looking for in the papyrus logs?

I would bet many of them are stuck in the "busy state" or similar situations were the scripts are looking for some variable to change but it never does until that script is restarted by reloading the mod or removing (stopping) the magic effect the script is connected to.

Skyrims Scripting system was not designed for the heavy use modders often need it to handle. Even the very best modders cannot avoid having issues forever if they are using complicated scripts.

Programing in this era with terabytes of code is not easy, not easy at all! The DEV made what was needed for their project goal for Skyrim under the deadline they had to meet. I understand that, but it still frustrates me as a combat modder.

However I am hoping the next game will have some of these issues changed for the benefit of modders as they (Bethesda) really does appreciate us modders.

I forgot to say that because of the multi threading, scripting is now much more challenging!

I see even veteran modders sometimes make some critical mistake in their scripts that can result in the script “getting stuck”.

Especially the scripts that are doing a lot of things at once. It is just too easy to forget. I read once that a programmer should not try to do more than 7 “things” at one time in their code because the human mind has a limit to consciously multitasking only about 7 things at once.

So you can see why it is not hard to make a mistake in a coding environment were hundreds of things are happening at one time.

I tried what you suggested spookyfix.com, and after uninstalling and reinstalling the mods, so far everything seems to be in working order again.
I'll see how it keeps going, but as for now the issue seems resolved.

Thanks for your help guys, would've never figured it out on my own^^

I have had the same random issue with Convenient Horses in the past. Using the console command 'stopquest ch' followed by 'startquest ch' made the hotkeys work again. (I'm not sure about the other mods, but maybe they too have a console command )

Is anyone that has these issue's ever using "quicksaves" or "quickloads" in their playthroughs?

Whilst I can't give exact details (there was a thread like 2 years ago), I remember something about always always loading saves from the Main Menu screen or even quitting Skyrim entirely.

I also vaguely remember that "quicksaves" are too quick, and often aren't able to properly save and store critical information - especially if you should happen to "quicksave" in the middle of a script thread.

I would never recommend doing this. Unless I am extremely out of the loop, this will cause many more problems than it solves (or appears to solve). I'd love it if some other community members could chime in on this

I dunno. I remember that advice back from Oblivion so I never use quicksaves. I've never has the mod functionality issue though.

you know i always use quick saves..super rearely used quick loads and you know i always start over for what not....im getting ready to start a new game after i beat wolfenstien:the new order and im gonna not use quick saves and see if i notice a difference.

My experience (even with Oblivion) is that is just an old wives tale. I always use quick saves (along side an auto save per my smart save mod) and I do not have any issues with them. But then I make sure my frame rate is not dragged down by HD graphics (and some mods) as I said.

In Skyrim it has been confirmed that Frame Rate and the scripts are tied together, low frame rate contributes largely to a poor environment for scripts to run.

Quicksaves were considered to be problematic by the modding community back in the Morrowind days. But my impression is that they are not the problem now that they were 13 years ago.

That said, I never do quicksaves. After so many years years it has become second nature to me to make full saves. It takes only a few extra seconds.

Good to know. I always update my PC specifically for the latest Elder scrolls. Maybe that's why I have so little troubles.

Quicksaves are harmless. Same with autosaves.

I can't believe people still blame quicksaves for potential problems in Skyrim.

When you use the regular main menu saving, you usually save the game into a new slot and [sometimes] remove some of the old saves if you need

The truth is the game is doing THE EXACT SAME THING when you do the quicksave:

Step 1) The game is writing the new quicksave as a NEW temporary file (.tmp)

Step 2) The game is renaming the exising quicksave to the backup file (.bak)

Step 3) The game is renaming the temporary file into the actual quicksave

So, how does it differ from the main menu saving?

Here is the step-by-step proof:

http://www.youtube.com/watch?v=0c7d8IY91Nc