I looked this up and could not find a past case where a user reported that when reopening a drawing, its coordinate system assignment was different than it was during the last session. And as you know, I could not reproduce this problem with your drawing and CSD files. If another user in the community has experienced this, maybe they can post their experience?
Otherwise, the only place to look would be your customization (LISP, etc.). Here in Product Support we do not work with customization, so you would need to investigate that with the creator of the custom code.
The reported problem is not related to any application that LISP. NET, etc..
changing the code of the coordinate system and effected directly by Autocad without any interference from custom application code.
I asked two colleagues if they have ever heard of a drawing's CS assignment changing upon drawing re-open, and neither of them have seen it happen either.
There is a new command in 2014 for un-assigning a coordinate system: GEOREMOVE. You could try running that to remove the CS assignment, then MAPCSASSIGN to assign your custom coordinate system again.