Why are `drush pm-list` & `drush pm-updatestatus` disabling the default theme?
Your themes for Drupal 7 should live here:


/sites/all/themes/THEMENAME - for all sites and all themes
/sites/example.com/themes/THEMENAME - for example.com of a multisite setup


Now in your case there is an additional note: You have the option to put your theme in a contrib and a custom subfolder. Themes in the custom subfolder would be skipped during the update process (see /r/drupal for cross reference). There is a caveat though: Apparently once you use contribyou also have to use custom otherwise it seems the whole tree breaks (see disqus)

Try to move the foo theme too: /sites/all/themes/custom/foo or /sites/example.com/themes/custom/foo then run drush rr and drush cc all