Create fields on hook_flush_caches().

I can confirm this with commerce 7.15-dev and Entity API 7.x-1.0. No license are issued.

Switching the priority to critical, since the module doesn't work if it's not fixed/explained.

I can't reproduce this. Your problem is that you're missing a field on the license entity type (did you create any custom types?) which should never be missing?

We should move the field creation code from hook_enable() to hook_flush_caches(), so that the missing fields are created on each cache clear, fixing the problem for edge cases like yours.

Can you try adding this to your commerce_file.module:

function commerce_file_flush_caches() {
  // Add the default license fields.
  commerce_file_license_configure_types();

  // Add line item fields for all line item types
  commerce_file_configure_line_item_fields();
}

And clearing cache?

This was done in 7.x-2.x (see https://drupal.org/node/1395488#comment-7658191)

Tagging for possible backport.