Kerbal Inventory/Attachement System - Parts wont rotate and are default to being upside down

[techgamer17]

Im trying to create a base core on the surface of Minmus, using all of the MKS duna modules. I kinda failed at dropping them off using the drop ship but the fix was to get kerbals to use KIS/KAS to turn them the right way up and orient them correctly. However, the game wont allow me to flip the module over without it being put into the terrain, which in turn then causes the module to either go several hundred meters in the air, or explode. 

 

Im not overly sure why this is happening and its prohibiting any further construction of my base, so if anyone knows a fix please can you say. Thanks. 

[DStaal]

KIS does allow you to 'translate' parts as well - Usually you can move them up a ways using the 'B' key, IIRC.