Here's some info, maybe it will help you with reproduction.
Spoiler
{"enabledMods": [
"SBTM",
"aitweaks",
"Adjusted Sector",
"advanced_gunnery_control_dbeaa06e",
"all_the_domain_drones+Vanilla",
"Cryo_but_better",
"aotd_vok",
"ashlib",
"BSC",
"ORK",
"CaptainsLog",
"lw_console",
"dynamictariffs",
"fast_engine_rendering",
"fleetsizebydp",
"IndEvo",
"lw_lazylib",
"leadingPip",
"lunalib",
"MagicLib",
"more_character_portraits",
"more_character_portraits_mods",
"more_character_portraits_vanilla",
"more_hullmods",
"advent_seven",
"objects_analysis",
"officerExtension",
"particleengine",
"sun_perilous_expanse",
"TAR",
"pt_qolpack",
"assortment_of_things",
"RetroLib",
"roider",
"scalartech",
"Seafood",
"second_in_command",
"swp",
"mayu_specialupgrades",
"alcoholism",
"Terraforming & Station Construction",
"US",
"unthemedweaponsutils",
"UGH",
"vic",
"audio_plus",
"shaderLib",
"Rouge_Redstar"
]}
Java 23, 4GB Ram allocated. Running below 60 FPS in hyperspace.
Since I have the bug, I could test a SiC version that removes "-30% to terrain speed penalty" from Navigation and report back if this indeed is the cause of the issue or not.
Figured it out. It's very likely framerate-dependent. If I have below 60 FPS and Idle 0% I get hit by storms while going slow with Navigation skill. I tested pure vanilla, SiC + libraries only and my modpack. Only the last case I got hit by storms, and it was the only game where I was below 60 FPS. Try loading up big enough modpack to drop FPS and try reproducing this that way. Adjusted Sector + lots of factions + Nex should do the trick.