Set Update Manager to install to sites/all/modules/contrib?
To circumvent these (and other) issues, I typically use the Drush command line utility to install and update new modules instead of the Update Manager.

For instance:

drush dl views --destination='sites/all/modules/contrib' # Download views to this path
drush dl uuid --destination='sites/all/modules/contrib' --select # Select other releases
drush en views views_ui  # Enable Views and Views UI
drush up ctools          # Update CTools


Drush also provides a number of other useful commands, and integrates very nicely with other modules. I highly recommend looking into using it if you haven't already!