Why do things randomly explode on the ground when I load a save?

[firefighter4443]

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Stats:

OSX 10.11.1

Macbook Pro (15-in, Mid 2010)

2.66 GHz i7

8GB 1067 MHz DDR3

NVIDIA GeForce GT 330M 512MB

KSP v1.0.4.861 (303 hours)

via Steam API: v017 (package versions: 1444853545)

Installed Mods:

KerbalEngineer v1.0.18.0

KerbalAlarmClock v3.4.0.0

I have built a modular base which is currently set up on the Mun. My plan is to take it to Ike, kill two contracts with one base, then take it all over the solar system with my space tug.

Anyway, it joins together on the ground with jr docking ports, and for flight with sr docking ports. However, its currently set up on a slightly inclined piece of ground, and it seems that when I exit to the space center, the jr docking ports default to perfect alignment. The problem is that when I load it again, this causes some of my modular base parts to load partially underground. It seems that when the physics load, it registers an impact, probably with the rover wheels, because they get destroyed, and part of my base flies up into the air a meter or two.

This is an image is of my base when stable (post-loading).

This is an image of my base when just loaded (prior to "impact"). Notice the left landing legs on the ISRU converter module, and all legs left of it, are 'submerged' underground.

This is a photo of it mid launch:

Interestingly, the drills do not register this 'launch' as movement, and continue drilling. If I raised the legs, they stop, but this event doesnt affect them.

Has this been solved? Can it be fixed?

Edited November 1, 2015 by firefighter4443
Added descriptions.