Hi there I,m having the exact same problem as you are, this is my second play through so I'm not totally crushed by the fact that I cant buy any of the houses as I've owned them all before but it certainly is rather annoying isn't it. I noticed you and I are using some of the same mods, I've included the list of the same ones I had installed at the time I first noticed the problem. My Skyrim is a Steam version and I also have all the DLC's Hearthfires, Dawnguard & Dragonborn, I'm using the new official 1.9 ledgendary patch and everything is all varified and up to date.
I'm really hoping some clever person can help us figure this silly little glitch out because it's really, really annoying. I have a mod called "Pimp my Proudspire"
http://skyrim.nexusmods.com/mods/9334 installed & I noticed by chance that it unlocks the door to the Proudspire mansion in Solitude so even if you don't actually own the house you may still be able to use it & there may be some other mods out there that do similar things for the other houses, it's worth a look I guess until someone fixes this bug.
Here is the list of mods we have in common, one of them could or "should" be the culprit but as yet I haven't figured out which one as disabling them at this point had no effect
-A Quality World Map
-Apachii Sky Hair
-Build Your Own Home
-Calientes Female Body Mod CBBE
-Cloaks of Skyrim
-Enhanced Night Skyrim
-High Quality Eyes
-More Village Animals
-UFO Ultimate Followers Overhaul
-Uncle Sheogoraths Really Helpful Hints and Tips
-Unofficial Skyrim Patch
-W.A.T.E.R Water And Terrain Enhancement Redux & the Dawnguard patch
SPECS:
Operating System: Windows 7 Ultimate 64-bit
Processor Intel(R) Core i7 CPU 960 @ 3.20GHz, 3193 Mhz, 4 Core(s), 8 Logical Processor(s)
Memory: 24 GB RAM
Available Physical Memory 21.2 GB
Total Virtual Memory 48.0 GB
Available Virtual Memory 44.9 GB
DirectX Version: DirectX 11
Mods List (If any links to the mods are needed, I can happily
provide them.)
The ones in BOLD were added after the issue began, so I am pretty sure they aren't causing it, but just in case, I've listed them as well.
I've also added my PC specs at the bottom in case that would be helpful.
-83 Willows, 101 Bugs
-A Quality World Map
-Apachii Sky Hair
-Babbettes Feats (Improved Cooking and Ingredients)
-Bandolier Bags and Pouches
-BFG Better Face Gen Female Face
-Birds of Skyrim
-Books Books Books
-Bright Purple and Deep Indigo Eyes
-Build Your Own Home
-Calientes Female Body Mod CBBE
-Calientes Vanilla Armor CBBE
-Camping Kit of the Northern Ranger
-Celine Outfit for CBBE
-Cloaks of Skyrim
-Dread Huntress Armor CBBE
-Dream Burros Asare Gothic Lolita Retexture (An armor)
-Hair Packs of Fallout
-Enhanced Character Edit
-Enhanced Night Skyrim
-Enhanced Slider Colors
-Feminine Running and New Dash Animation
-Field Mage Outfit
-Hair Packs of TES Oblivion
-HD Textures DLC Fix
-High Quality Eyes
-Improved Fish
-Lanterns of Skyrim
-Midas Magic
-More Village Animals
-Pets of Skyrim
-Pretty Face
-Pretty Female Idles
-Project Reality- Climates of Tamriel
-Rans Character Gen Morph
-Roosters at Dawn
-Snow HQ Textures
-Snow White Vampires
-Solitude Public Bathhouse
-Spouses can live everywhere
-Sunglasses
-Roadstroakers Rogue Sorceress Outfit CBBE
-Thieves Guild Duelist Armor
-Triss Armor
-UFO Ultimate Followers Overhaul
-Uncle Sheogoraths Really Helpful Hints and Tips
-Unlimited Bookshelves
-Unofficial Skyrim Patch
-Victorias High Heeled Walk
-W.A.T.E.R Water And Terrain Enhancement Redux
-Wearable Lanterns
SPECS:
Operating System: Windows 7 Home Premium 64-bit
Manufacturer: Toshiba
System Model: Satellite L755
BIOS: InsydelH20 Version 03.60.453.40
Processor: Intel(R)-Core(tm) i3-2350M CPU @ 2.30GHz (4 CPUs), ~2.3GHz
Memory: 4096MB RAM (4 GB RAM)
Page File: 4962MB used, 3123mb available
DirectX Version: DirectX 11