Fessels,
Where do you have Armoured Horses loaded? Before or after Convenient Horses? I ask because my horses no longer have their armour.
I know BOSS always loaded it in the wrong place when I was using a different horse mod for followers and I had to move it to get them to show up. BOSS loads it after Convenient Horses which is at the top. I see people are asking in the Armoured mod about the same thing and the 1.6 patch, but just going by the comments I don't think they know much about load order. It worked for me with the patch before I changed over mods so it's not that.
I'll try moving it again anyway. Just wondering since I see one of your screen shots with the armour on.
My load order, just for interest sake. It's probably pretty tame compared to some, but I don't want to jinx things by adding too many more just yet.

Plus, I'm keeping an eye on the Unofficial Patch thread to see what's going to happen there as I uninstalled it per their advice for the time being.
I'll probably remove the Essential Followers and Horses esp since Convenient Horses does it and I don't care about followers now, except for Meeko, and Essential Followers has a separate esp for the dogs.
By the way, Birds of Skyrim is awesome for some ambiance in cities, farms and around waterways. Pigeons in the cities made me laugh. Every city needs pigeons.
http://skyrim.nexusmods.com/mods/17723
@ MasterAub,
Thanks Maigrets for the updates on this...
So...I guess I am trying this SkyRE soon...

My eyes glazed over when I was reading all the changes it makes and there isn't a proper readme as such, but after installing FCOM this is a breeze. When you see all the new perks and other good stuff, I think you will like it.
There's even a perk tree for vampires, but I didn't install that plugin because I don't want to be a vamp. Makes me scared of the sun...
There are also a heap of new spells, including Unlock spells for mages which is something I miss from Oblivion. Also some excellent Conjuration and other spells as well. Good old Farengar made some money off me for those and I'm trying to save to get the Whiterun house which will have to wait now since I bought a horse as well.