Order shows "Completed" but under Licenses it's not assigned

Something is wrong with your PayPal setup.
After the transaction has completed, the "order has been paid in full" event should fire, and commerce_license should respond and activate the license.
One of these didn't happen, so your license remains untouched.

I remember someone having and solving a similar issue, but I can't find the issue now, you can try searching for it in these queues (commerce_file, commerce_license).
What might help is going to admin/config/workflow/rules/settings and enabling "Log debug information to the system log", then looking at the debug in admin/reports/dblog to see if the event was fired and if commerce_license responded.

Hello.

I have a similar issue.

I've activated the debug on rules and on "order has been paid in full". the event fires, but no license is assigned.

This is happening since the last update.

Debug info

This happens to me with paypal also, this is the debug report. I can't , I am afraid, make much sense of it
when I use the example payment module.. all is fine

Message Rules debug information:
" Reacting on event After updating an existing commerce order.

0 ms Reacting on event After updating an existing commerce order.
9.512 ms Evaluating conditions of rule Commerce order message: changing status. [edit]
11.977 ms The condition data_is evaluated to FALSE [edit]
11.99 ms AND evaluated to TRUE.
" Rule Commerce order message: changing status fires. [edit]
0 ms Rule Commerce order message: changing status fires.
6.664 ms Evaluating the action entity_create. [edit]
7.8 ms Added the provided variable message of type message [edit]
10.512 ms Evaluating the action data_set. [edit]
37.501 ms Evaluating the action data_set. [edit]
40.699 ms Evaluating the action data_set. [edit]
40.97 ms Rule Commerce order message: changing status has fired.
53.103 ms Evaluating conditions of rule Delete shipping line items on shopping cart updates. [edit]
53.515 ms The condition data_is evaluated to FALSE [edit]
53.527 ms AND evaluated to FALSE.
53.564 ms Saved message of type message.
64.724 ms Finished reacting on event After updating an existing commerce order.

" Reacting on event Completing the checkout process.

0 ms Reacting on event Completing the checkout process.
0.313 ms Evaluating conditions of rule Update the order status on checkout completion. [edit]
0.325 ms AND evaluated to TRUE.
" Rule Update the order status on checkout completion fires. [edit]
0 ms Rule Update the order status on checkout completion fires.
0.171 ms Evaluating the action commerce_order_update_state. [edit]
" Reacting on event After updating an existing commerce order.
0 ms Reacting on event After updating an existing commerce order.
0.288 ms Evaluating conditions of rule Commerce order message: changing status. [edit]
0.821 ms The condition data_is evaluated to FALSE [edit]
0.833 ms AND evaluated to TRUE.
" Rule Commerce order message: changing status fires. [edit]
0 ms Rule Commerce order message: changing status fires.
0.451 ms Evaluating the action entity_create. [edit]
0.866 ms Added the provided variable message of type message [edit]
1.137 ms Evaluating the action data_set. [edit]
3.921 ms Evaluating the action data_set. [edit]
6.43 ms Evaluating the action data_set. [edit]
6.694 ms Rule Commerce order message: changing status has fired.
7.588 ms Evaluating conditions of rule Delete shipping line items on shopping cart updates. [edit]
7.766 ms The condition data_is evaluated to FALSE [edit]
7.777 ms AND evaluated to FALSE.
7.813 ms Saved message of type message.
12.061 ms Finished reacting on event After updating an existing commerce order.
40.132 ms Rule Update the order status on checkout completion has fired.
40.597 ms Evaluating conditions of rule Activates licenses of a free order. [edit]
45.981 ms The condition commerce_payment_order_balance_comparison evaluated to FALSE [edit]
45.995 ms AND evaluated to FALSE.
46.148 ms Evaluating conditions of rule Assign an anonymous order to a pre-existing user. [edit]
46.669 ms The condition data_is evaluated to FALSE [edit]
46.68 ms AND evaluated to FALSE.
46.852 ms Evaluating conditions of rule Create a new account for an anonymous order. [edit]
47.249 ms The condition data_is evaluated to FALSE [edit]
47.26 ms AND evaluated to FALSE.
47.378 ms Evaluating conditions of rule Commerce order message: order notification e-mail. [edit]
47.389 ms AND evaluated to TRUE.
" Rule Commerce order message: order notification e-mail fires. [edit]
0 ms Rule Commerce order message: order notification e-mail fires.
2.594 ms Evaluating the action entity_create. [edit]
2.997 ms Added the provided variable entity_created of type message [edit]
3.58 ms Evaluating the action data_set. [edit]
3.945 ms Evaluating the action entity_save. [edit]
4.027 ms Saved entity_created of type message.
11.982 ms Evaluating the action message_notify_process. [edit]
584.118 ms Rule Commerce order message: order notification e-mail has fired.
631.602 ms Finished reacting on event Completing the checkout process.

Update,
I think for me it is a simple as taking the site out of maintenance mode , some info here
https://drupal.org/node/1902660

I see no remaining issues here.