I love this mod guys, but.....
Try a scramble mission with Spits Mk II, Spits Mk Vc 2-cann and Hurricanes Mk 1 in QMB, I find 1st time I play the mission (without leaving QMB) its ok but on (sometimes 2nd) 3rd and subsequent 'refly' the Mk II Spits collapse one side of their gear and the Hurricanes collapse both sides of their gear immediately at the start of the mission, the Mk Vc Spits appear ok as far as I can tell.
I've tried other scramble missions with different planes and they appear ok, but as you say there's a million mod combinations, and a lot of planes to try in scramble QMB missions too!.
I'm using following mods in MODS folder , under UP2.01:
00_A_Plutonium_Maximum_Effects_Edition_V1
00_GearDamageFX
00 HG&P_Richochet_Gunsmoke_Bullets_2d_Smoketrail
0_Bomber_crew_mod_UP2.0
0_Wolfighter_Gore4allPlanes_v1.4
AdvanceDamageFX4CanopybyWolfighterV1.2
Arado234C2
Cant1007_SASver
Combined_Planes_Contrail_Fix_V2
CY6_Skyraiders
He-219
J7W1
Jivers Total Sound Modv1.0
Lancaster
Me-262B-1a
ME-410-Nightfighter
QMBpropal
STD
WellingtonMk_III
In JSGME I have the following activated:
00_Bullets_IntermittantSmokeTrail
00_Ercan_Wide
00_EFFECTS_High
00_Hackenkruz_Enabler
00_Perfect_Map_Textures
00_ZloyPetrusko_AAAmod_fast
00_RealisticBomb&TorpedoFusing
A few other people seem to be getting similar issues, so hope the above is a bit more specific to help. I do like the mod a lot so good luck! Maybe you can point at a mod to deactivate to try out and I'll see what I get.
Z