In a previous installation I had the same glitch with vessel being released on different orbit, so I started narrowing down the incompatible mod.
I tried installing via CKAN only HANGAR.
It worked.
Then I added Astronomer Visual pack, his dependencies and Chatterer and trying the same mission when trying to deploy the stored vessel, an aler pop up saying
"vessel clearance is insufficient for safe launch".
Hope this can be of help for someone more proficient than me.
GAME VERSION 1.3.1, List of mod
Astronomer's Visual Pack (AstronomersVisualPack v3.63)
Astronomer's Visual Pack-8k Textures (AVP-8kTextures v1.6)
AT Utils (AT-Utils v1.5.0)
Chatterer (Chatterer 0.9.93)
Community Resource Pack (CommunityResourcePack 0.8.0.0)
Configurable Containers Core (ConfigurableContainers-Core 2.4.1.2)
Environmental Visual Enhancements (EnvironmentalVisualEnhancements 2:EVE-1.2.2-1)
Ground Construction (GroundConstruction 1.2.1)
Ground Construction Core (GroundConstruction-Core 1.2.1)
Hangar (Hangar 3.3.3)
Kopernicus Planetary System Modifier (Kopernicus 2:release-1.3.1-7)
LoadingScreenManager (LoadingScreenManager 1.2.3.4)
ModularFlightIntegrator (ModularFlightIntegrator 1.2.4.0)
Module Manager (ModuleManager 3.0.4)
scatterer (Scatterer 2:v0.0324)
scatterer - default config (Scatterer-config 2:v0.0324)
scatterer - sunflare (Scatterer-sunflare 2:v0.0324)