Xmodmap customization disappears after TTY visit

I'm using Xmodmap to customise some non-standard keys on my keyboard. Using GDM to get X, I am running Xmodmap ("xmodmap $HOME/.xmodmap") as a startup job in gnome-session-properties.
The customisations work well, but if I leave X and then return -- say, to check on of the *top programs running in a TTY -- the Xmodmap customisations are gone. Mind you, I haven't quit X -- it's still running on ctrl-shift-f1 -- and I'm not expecting to see X configuraions on the TTY. I'm simply expecting the customisations to still be there when I return to my still-running X session.
Any suggestions as to why this happens and how to remedy it? I know, I could just skip using TTYs but well, I like 'em and I'd prefer not to.

I don't use GDM but this page (https://wiki.ubuntu.com/CustomXSession) makes me think that maybe GDM is running a pre-defined session that overwrites your xmodmap configuration when you switch back from a tty. Try creating a custom xsession and see if that works

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Xmodmap customization disappears after TTY visit

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