serious linking problem! help!

I have been having a problem with linking in the levels of SuperTux3d:
After a save all linked groups will suddenly be local. Like if I had used the “Pack All”
button in the Main Menu.
Only I didn’t. Blender just decided that it needed to be done.
(I’m not sure what makes one save do this but not the one before.)

I use linking in the same way that YoFrankie! does (since I built off of YoFrankie!)
so I have the main character linked in, the badguys linked in,
the bonuses linked in, … .
After Blender decides that groups need to be local, I can’t change the
main character, or anything else, and have it reflect in the broken level the way
it should.

About the fastest way to fix this I have found is to unlink all groups, then relink them
from outside. Then I have to go through and fix each broken group-instance empty.

Does anybody know how I could get around this? It looks like a bug in the Blender
code to me. Is it - I hope - a feature, that I just need to learn how to use?

And does anybody else have this problem?

I’ll submit a bug report in a minute.