Ah, I see where I went wrong.
Environment variables set in ~/.profile need to be exported in order to
be present in x-session-manager and all its descendants. (Whereas they
will be present in login shells even when they are not exported.) The
line 'PATH=~/bin:"${PATH}"' (no export) and the fact that everything
worked as expected when logging in on the virtual console made me think
that those variables did not need to be exported.
After adding the appropriate "export" commands everything works fine.
Sorry for bothering you and thanks for your efforts!
--
Feature Request: Provide a single configuration file for user settings
https://bugs.launchpad.net/bugs/134378
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