Had an issue on a client machine where although Document IDs were enabled on the site collection, no IDs were being applied to the uploaded files.
SharePoint assigns these IDs as part of a timer job that runs in Central Administration. To fix this you will need to run the following two jobs:
Document ID enable/disable job
and
Document ID assignment job
for each site collection where this is not working. You can view the timer jobs in Central admin from this page:
/_admin/ScheduledTimerJobs.aspx
Hope that helps!