I don't have trouble with that.
But this might mean nothing, because I'm on a German version of InDesign CS6 v8.1.0 on Mac OSX 10.7.5.
What I try to do:
Change the preferences.
Change the workspace.
Restart your machine.
The preferences should be sticky then…
In order to set the units as the default for new work you must do so with NO FILES OPEN.
Resetting units in the prefs will not affect existing files.