RE: Checklink & reconcile Inventory
Look in Admin->Routines->master posting? This is supposed to list all batches including some stuck in processing. You may need to recover and complete those batches.
Worst case, you can go into SY0500 in the Dynamics database and manually delete those batch headers. This will not delete the detail, just the header that shows the batch as stuck.
As for the users, some people do not exit properly. First place to look is Administration->Utilities->System-> User activity to see if GP thinks anyone is logged in. You can delete those users if needed.
Otherwise, the user can be stuck in SQL. I always recommend shutting down and restarting SQL if nothing else works (of course at night when no one is supposed to be logged in)