This problem has been hidden by 16603, but still exists:
I have an offline circulation file which was generated by the Windows offline circulation program. If I upload this file and choose "Add to offline circulation queue" it works as expected.
If I upload the same file and choose "Apply directly," the process never completes. Firebug shows a seemingly never-ending series of calls to /cgi-bin/koha/tools/background-job-progress.pl?jobID=8c20822320e5fbd7579aa1f61411ba00 but nothing happens.
Note that even if Plack is enabled, this page is processed directly by Apache :
ProxyPass "/cgi-bin/koha/offline_circ/process_koc.pl" "!"
This may have some effect.