This is happening inconsistently, but often enough to be a problem.
So far, we have come across two issues with it:
#1 - A new user registers for the site. That user is then taken to a CiviCRM form for them to choose their payment level. Sometimes, the user is logged out between the drupal registration form and the CiviCRM form, leading to them being prompted to log in again when they reach the Civi payment form.
#2 - Background: We are currently testing some changes to our site, and so the admins all have multiple accounts, most of which have admin permissions.
An admin logs into the drupal site, and then goes to CiviCRM. For some reason, though, they are logged into one of their other admin accounts on CiviCRM. They go to "Find a member", and then click the link to the member's drupal profile. When Civi takes them back to drupal, it throws an error because they are logged into a different account on Drupal than on Civi.
We are using Drupal 7 and CiviCRM 4.6.28