As I look at co_base_ice_large02.cmp I see that HpDockMountA is right on the base door xvalue=-811.9, HpDockPointA02 is about 4-5 ship lengths (eagle) from the door xvalue = -1034.1, and HpDockPointA01 is between the two at xvalue = -953.4

So, should those values you indicate be reversed? ie. HpPointA02 at 400 and HpMountA at 200?

Oh, forgot you run a mod that players can join without the mod.
Here is the declaration:

[Solar]
nickname = co_base_ice_large02
ids_name = 1
ids_info = 1
type = STATION
DA_archetype = solar\dockable\co_base_ice_large02.cmp
material_library = solar\Solar_mat_co_base.mat
LODranges = 0, 20000
mass = 10000.000000
open_sound = depot_open_sound
close_sound = depot_close_sound
docking_sphere = berth, HpDockMountA, 2.500000, Sc_open dock1
docking_sphere = berth, HpDockMountB, 2.500000, Sc_open dock2
docking_sphere = berth, HpDockMountC, 2.500000, Sc_open dock3
docking_sphere = moor_medium, HpDockMountD, 5.000000
docking_sphere = moor_large, HpDockMountE, 10.000000
docking_camera = 0
solar_radius = 500
shape_name = NNM_SM_DEPOT
hit_pts = 999999961690316250000000000000000000.000000

Your capships will undock from D and E (but this depends on what you have changed from vanilla). My mod is highly tweaked, I allow capship docking on bases and made special docking arrangements for them that may not work on your vanilla setup.

Best thing I can say is experiment and keep a vanilla backup if you need to revert.

As you noted, capships, no matter how they dock, can indeed UNDOCK from the berths (unless you have gone to extraordinary length to lock them into moors). This is why you are getting hung up, probably on the door or the controller window. I use fast docking and extended ranges and special docking methods, see what works best for you.

The dock points you referenced are correct, I had them reversed them in my first response. Fixing that now...

On mine, Capship undocking is random. Undock 6 times and 3 will be from berths and 3 from the med_moors

that moors.dll is your best best robo..

anything else is a mountian of work in comparison, that addon will gain you extra functionality and solve your undocking problem.

You simply assign a dockpoint to be the moor in the base .ini
Then you tell the big ships to use moors when docking.

Tweak to taste,

Problem solved.. and im pretty sure it'll work with FLAC or anything really like most of Adoxa's extra's

Well, taking a step back...
Moors works great, ships dock and undock from the moors rather than the berths which fixes the original problem. The problem now is that moors.dll seems to take precedence over FLAC's ability to block/allow docking by ship type. The bases in New London are set to allow only FIGHTERS and FREIGHTERS to dock but capships (CAPS) are able to dock using the moors.

I'm going to double check everything to make sure I have things configured properly.

If docking is not an issue, move the HpMount on the ships that exhibit this behaviour 200m below the ship, as suggested earlier in the thread. This will cause the ship to undock 200m above the base, likely well clear of it.

If you had been using FlHook, the "moors" plugin by Adoxa is an option - it makes capital ships using medium and large moors undock in reverse, like the vanilla transports do.