Bottom node (to attach launch clamp) is moved upward inside vessel

[Gordon Dry]

What could be the reason for this?

Exiting to VAB and reentering didn't help.

Log:
https://www.dropbox.com/s/riq13lk1qewo4p7/2018-04-02_1 KSP.log.7z?dl=1

[Barar]

Are you connecting to a spare node on the shroud?, I know some items have multiple nodes. I haven't used those launch clamps before so not sure, it might be a bug with the part. You can try using this NodeHelper to adjust the node easily, watch out if rescale is anything other than 1.0, as it changes the node values you get.

Looking at your log file, you do have an unrelated 2877 errors. Looks like Editor action group doesn't like Click Through Blocker and spams this in VAB/MAB. Might make you lag in game. 

  NullReferenceException: Object reference not set to an instance of an object
  at KSP.UI.Screens.EditorActionGroups.ConstructGroupActionList () [0x00000] in <filename unknown>:0 
  at KSP.UI.Screens.EditorActionGroups.ConstructGroupList () [0x00000] in <filename unknown>:0 
  at KSP.UI.Screens.EditorActionGroups.ClearSelection (Boolean reconstruct) [0x00000] in <filename unknown>:0 
  at ClickThroughFix.CBTMonitor.Update () [0x00000] in <filename unknown>:0