When ordering from a staged file you see all funds ever used in the system - including ones that have since been marked inactive. This does not happen with any other type of order - just the order from staged file: /cgi-bin/koha/acqui/addorderiso2709.pl?import_batch_id=59&basketno=7&booksellerid=1
This is also a bug in master - the list of funds should match the one you get when creating an order from the other options.
This will certainly fixed by bug 7180 and bug 10875.
*** This bug has been marked as a duplicate of bug 10875 ***