fix #9934: adjust query options once pagination is done (rebased)

Fixes http://trac.openmicroscopy.org.uk/ome/ticket/9934 -- in trying to replicate it, make sure you use the gist revision linked from the ticket.

--rebased-from #1456

Also fixes FS-specific tests in `PojosServiceTest` such that now all the tests in the class should pass.