This has caught me out once to often (usually when creating a high-poly from a low), its a real nuisance. Is there some sort of script or tick box to change it?
I'm well out of my depth here, I couldn't find the files they listed ("...\enu\defaults\currentdefaults.ini"), but I found the following via "Local Disk (C:)> Program Files> Autodesk> 3ds Max 2014> en-US> defaults> MAX> FactoryDefaults":
Replies
https://forums.autodesk.com/t5/3ds-max-forum/instances-as-default/td-p/4171406?nobounce#
; ObjectCloneType
; 0 = Copy
; 1 = Instance
; 2 = Reference
[TransformTool]
; Copy
ObjectCloneType=0
C:\Users\USERNAME\AppData\Local\Autodesk\3dsMax\20XX - 64bit\ENU\en-US\defaults\MAX\
; 0 = Copy
; 1 = Instance
; 2 = Reference
[TransformTool]
; Copy
ObjectCloneType=0