"drush up" turns off all of my modules I'm using drush to make version updates and any time a module (in todays case, recaptcha) needs to be updated, it successfully does the update.  However it seems to reset the database turning off every single non-core drupal module.

I cant find anything about this on the internet anywhere. Anyone have any ideas?
When you run drush up, you are actually updating Drupal core along with contrib modules and themes. Try:
drush up recaptcha -y
This will update the recaptcha module only, with no confirmation needed.