I am not using any MODs or extensions at all, excep the Egosoft 2 DLC and mine which is just doing more meaningfull debug_text to investigate those issues.
For the adjacent zone, I am in Cold Star (my translation because my game is in french). My zone is between zone-2 and 3, but north of it It is very close to the both of them. It is a non populated free zone. The kind you light up on the map as you travel the map. I put my warehouse there because it is near the asteroids in zone-3 and 2.
I did a thread about this where I am talking about the bug of warehouses using mining ships. I always use the same savegame file where my ware house has no mining ships. As soon as I load my savedgame, I assigned all mining ships to my warehouse (all kinds of ships) and then just let it go for a while. I then take the log and check what happened. The easiest visual clues are on ship travelling from zone-2 to mine in at least 30 min. The second visual clue is ships that are either full or empty and not doing anything, not even returning to homebase. Those symptoms lasts for 15-60 min, depending on the ship.
Here are a bit more log info from the long traveling case. Notice the distance it is sayng before travelling from one sector to another one next to it: 1123.5m away
[Scripts] 23234.63 *** aicontext<mining.ship.station,0x119c9>: this.ship.knownname=Miner-Large-Vrak
[Scripts] 23234.63 *** aicontext<mining.ship.station,0x119c9>: this.ship.cargo.capacity=290000
[Scripts] 23234.63 *** aicontext<mining.ship.station,0x119c9>: this.ship.commander.exists=1
[Scripts] 23234.63 *** aicontext<mining.ship.station,0x119c9>: homebase=0x120be
[Scripts] 23234.63 *** aicontext<mining.ship.station,0x119c9>: this.ship.commander=0x120be
[Scripts] 23234.63 *** aicontext<mining.ship.station,0x119c9>: warebasket=[ware.crystals,ware.ice,ware.nividium,ware.ore,ware.silicon]
[Scripts] 23234.63 *** aicontext<mining.ship.station,0x119c9>: warebasket.count=5
[Scripts] 23234.63 *** aicontext<mining.ship.station,0x119c9>: this.ship.cargo.free=16704
[Scripts] 23234.63 *** aicontext<mining.ship.station,0x119c9>: [Ship=Miner-Large-Vrak, Mining] returning to Warehouse EF in My Testing Sector...
[Scripts] 23234.63 *** aicontext<move.generic,0x119c9>: Long distance trip. Using engine booster...
[Scripts] 23234.63 *** aicontext<move.nohighway,0x119c9>: this.zone = Reprise de l'Extraction, $target = Warehouse EF, $targetzone = My Testing Sector
[Scripts] 23234.63 *** aicontext<move.nohighway,0x119c9>: current position in zone: position.[-35914.246094m, -4127.008789m, 36205.902344m]
[Scripts] 23234.63 *** aicontext<move.nohighway,0x119c9>: moving to zone exit pos: position.[-34967.457031m, -3961.002441m, 36787.765625m], 1123.5m away
[Scripts] 23256.36 *** aicontext<move.nohighway,0x119c9>: 23256.363 boost from position.[-35916.433594m, -4127.155273m, 36209.964844m] in Reprise de l'Extraction to position.[17011.656250m, 342.930634m, -386.853333m] in My Testing Sector which is 16732m away
[Scripts] 23256.36 *** aicontext<move.nohighway,0x119c9>: 23256.363 BOOOOOOOOOOOST!
[Scripts] 23643.70 *** aicontext<move.nohighway,0x119c9>: 23643.703 STOOOOOP!
[Scripts] 23643.70 *** aicontext<move.nohighway,0x119c9>: 23643.703 now in zone My Testing Sector at position.[17010.765625m, 342.928711m, -388.274231m]
[Scripts] 23643.70 *** aicontext<move.generic,0x119c9>: boost complete. Moving into final position.
[Scripts] 23643.70 *** aicontext<move.generic,0x119c9>: Short distance trip to position.[25000.000000m, -2161.943359m, 0.000000m] in My Testing Sector. D=8380, using highways: 0
[=ERROR=] 26854.31 aicontext<move.generic,0x119c9>: Not successfuly reached the position in targetzone My Testing Sector(0x12033)! Miner-Large-Vrak(0x119c0) is currently in Bout de la Ligne(0x111a7), 72304m from the target destination (actual distance 72128).
[Scripts] 26856.55 *** aicontext<mining.ship.station,0x119c9>: [Ship=Miner-Large-Vrak, Mining] Homebase is Warehouse EF in My Testing Sector(La Carrière), we are at position.[35814.101563m, 481.064148m, -11691.822266m] in Bout de la Ligne(La Carrière), distance to homebase is 72192
[Scripts] 26856.55 *** aicontext<mining.ship.station,0x119c9>: [Ship=Miner-Large-Vrak, Mining] moving to park at homebase Warehouse EF
[Scripts] 28934.49 *** aicontext<mining.ship.station,0x119c9>: [Ship=Miner-Large-Vrak, Mining] now parked at homebase Warehouse EF
[Scripts] 28934.49 *** aicontext<mining.ship.station,0x119c9>: [Ship=Miner-Large-Vrak, Mining] reserved 14672 Silicium for unloading at homebase Warehouse EF(0x120be) (have 14672, homebase has room for 265664)
Here something else that did not happen in the previous game sessions. It looks like it did not go through the same scripts as above so I have no clues what it did between the 2 lines. I would need to investigate deeper. This log was created last weekend.
Line 99: [Scripts] 23228.14 *** Context:md.Orders.SectionHandler_Broadcast<inst:26b1e>: attempt to set 0x120be Warehouse EF as commander of 0x119c0 Miner-Large-Vrak old commander null
Line 8501: [=ERROR=] 26854.31 aicontext<move.generic,0x119c9>: Not successfuly reached the position in targetzone My Testing Sector(0x12033)! Miner-Large-Vrak(0x119c0) is currently in Bout de la Ligne(0x111a7), 72304m from the target destination (actual distance 72128).
Line 16476: [Scripts] 29269.24 *** aicontext<mining.ship.station,0x119c9>: [Ship=Miner-Large-Vrak, Mining] updating warebasket on Miner-Large-Vrak(0x119c0) to collect [ware.crystals,ware.ice,ware.nividium,ware.ore,ware.silicon]
Line 21768: [Scripts] 30568.70 *** aicontext<move.collect.drone,0x101b988>: 30568.7 returning to homebase Miner-Large-Vrak[0x119c0] in Reprise de l'Extraction (dronelaunchpad)
Line 21774: [Scripts] 30569.31 *** aicontext<move.collect.drone,0x10287de>: 30569.31 returning to homebase Miner-Large-Vrak[0x119c0] in Reprise de l'Extraction (dronelaunchpad)