The cron is run via CLI, so Apache does not handle the request, and your virtual directories are not known. The virtual directory aliasing only occurs with Apache, so you should either remove the virtual directory aliasing to Blesta's directory so the path can be determined correctly via CLI, or run the cron via wget so that it will use Apache instead.
If you opt to remove the alias to Blesta (i.e. rename the 'blesta' directory to 'services') and you get a 'license invalid' page when you try to login, then you just need to reissue your license key. To do this, log into your account, click to manage the service, check the 'Reissue' checkbox and save. Then the license will revalidate at the new location when you login to your installation.