Arrowmaster wrote this on Reddit:
The following parts are all marked as being ignored by physics simulations and have 0 mass in flight.

• Science experiment sensors (only the small sensors, not the goo or materials bay)
• Lights
• Communotron 16 antenna
• Communotron 88-88 dish
• Ladders
• 1.25m to 0.625m adapter plate
• Small Hardpoint
• Cubic Strut
• Octo Strut
• Struts
• Radial Attachment Point
• Small landing gear
• RCS thrusters
• OX-STAT solar panel
• Small and large radially attached batteries (wtf squad?)

I had discovered that's VAB or SPH (and your mod) apply these parts weight while preview center of mass.

Could you fix this problem ?

Thanks for the report, this is already fixed on master.

I confirm issue for large radial battery and cubic strut. Not tested/checked anothers parts yet... Do you need I do it ?
Nb: I feel "Small Gear Bay" could be probably ignored too.

Like I said, is fixed on master. If you didn't compile the master branch then you aren't going to see the fix.

I don't know how to compile myself. But I see you had published new release, thank you :)