Two designs with identical components have different weights. The only difference between the two is the classing as commercial or military vessel (here grav and geo survey sensors respectivly).
In the case of the commercial vessel the engines and the jump drive seem to be significiantly lighter, although the speed and 'exact class size' is calculated correctly. The TCS is different, however.
Haven't built these designs yet so I don't know if this is just a visual bug with weight or perhaps connected with the speed issues mentioned by Erik.
Zambia II class Geosurvey Ship 1,038 tons 111 Crew 503 BP TCS 20.75 TH 500 EM 0
6024 km/s JR 1-25(C) Armour 1-23 Shields 0-0 Sensors 1/1/0/5 Damage Control Rating 1 PPV 0
MSP 76 Max Repair 300 MSP
Sutton Carrier Alliance Commercial Jump Drive 4500 Max Ship Size 4500 tons Distance 25k km Squadron Size 1
NQEA Internal Confinement Fusion Drive (2) Power 250 Fuel Use 4% Signature 250 Armour 0 Exp 1%
Fuel Capacity 100,000 Litres Range 1084.3 billion km (2083 days at full power)
Phased Geological Sensors (1) 5 Survey Points Per Hour
This design is classed as a Commercial Vessel for maintenance purposes
Turkmenistan II class Gravsurvey Ship 4,150 tons 111 Crew 503 BP TCS 83 TH 500 EM 0
6024 km/s JR 1-25(C) Armour 1-23 Shields 0-0 Sensors 1/1/5/0 Damage Control Rating 1 PPV 0
Maint Life 0.96 Years MSP 76 AFR 137% IFR 1.9% 1YR 80 5YR 1194 Max Repair 300 MSP
Sutton Carrier Alliance Commercial Jump Drive 4500 Max Ship Size 4500 tons Distance 25k km Squadron Size 1
NQEA Internal Confinement Fusion Drive (2) Power 250 Fuel Use 4% Signature 250 Armour 0 Exp 1%
Fuel Capacity 100,000 Litres Range 1084.3 billion km (2083 days at full power)
Phased Gravitational Sensors (1) 5 Survey Points Per Hour
This design is classed as a Military Vessel for maintenance purposes
*edit*
I've tried exchanging the engines (for ion engines) and the military/commerical classification reason to weapons. In both cases the weight was calculated correctly for the military vessel. I don't know the code, but I guess this pins the reason down to be something with the classification.
*edit2*
Applied speeds during surveys etc. match that of correctly calculated weight, if I look at the ship details (F6) the max speed is however listed as 24096 km/s (Zambia II class).
In F12 the speed seems to be the correct one (6024)
unless clicking on the ship in F6:
The Zambia II 001 I checked for its max speed can now fly at 24096 while the Zambia II 002 I haven't yet clicked in F6 can only fly at 6024.
Activating the Zambia II 002 in F6 allowed it to fly 24096 km/s which it now does automatically if I give it any orders.