What the title says. The weather changes abruptly, as if there was no fade between the two styles. So cloud will go from lightly covering the sky to full overcast in a split second, changing the lighting and everything.

These are the mods I have installed:

Skyrim.esm
Update.esm
WARZONES - Civil Unrest.esm
Shadow Striping Fix.esp
SMIM_Fixes.esp
SoS - The Dungeons.esp
SoS - The Wilds.esp
Realistic Lighting.esp
Realistic Lighting Patcher.esp
Warmer Magic Lights v2 - Big.esp
Real Lights - Cities.esp
Birds.esp
dD - Enhanced Blood Main.esp
morevillageanimals.esp
Real Wildlife Skyrim 0.1.esp
SIM - NPCAdditionsHOSTILE.esp
SIM- NPC Additions.esp
SIM - NPCSUBMITTED.esp
SIM - Waterbugfix.esp
Water FX - Get Wet.esp
whiteruntrees.esp
BurntCorpse.esp
HoodsAndCirclets.esp
JMO-Dragons.esp
RealisticWaterTextures.esp
Reduced Distance NPC Greetings.esp
dD - Realistic Ragdoll Force - Realistic.esp
ReneersCrimeOverhaul.esp
DeadlyCombat.esp
Dual Wield Parrying_RandomAttacks.esp
Killmove +.esp
Balanced_Alteraton.esp
Balanced_Conjuration.esp
Balanced_Destruction.esp
Balanced_Illusion.esp
Balanced_Restoration.esp
Balanced_Magic_Adept.esp
Balanced_Magic_Novice.esp
Balanced_Magic_Master.esp
MoreOrganicCities.esp
OpenFaceGuardHelmets.esp

The rest are texture replacers,w hich I doubt would effect weather transitions?

update.esm... I'm surprised you have this on your list. Is it active? As far as I know, this was the first patch, released by Bethesda on day one. Later patches, went directly to Skyrim.esm, rendering the need for an update.esm, obsolete. So:

• Start by moving update.esm AND update.bsa out of your Skyrim folder.
  
• For the time being, don't use any mod manager. Skyrim's latest patch changed the way, load order is being handled and all mod-related utilities have to be updated.
  
• Check the load order, as it's being listed on Skyrim Launcher and try to refine it. Put fixes on the top of the list and the rest, below them.

If your game insists on this behavior, start deactivating mods one by one, to find the one which causes this.

Found it, ENB cloud intensity does it. disabled that in my enbseries.ini

Good to know m8