Using pre-synthesis and post-fit taps is supported but requires some thought. Whenever you tap a NEW pre-synthesis node in a partition, Quartus II wants you to set your netlist type to source. It needs to explicitly preserve this node in most cases. Think of it like compiling your C++ source files with debugging symbols. You can set the netlist type to Post Synthesis or Post Fit after the compile and the node will still be preserved.
When you compile from the source, Partition Merge will complain that you're tapping post-fit nodes in a partition with the wrong netlist type. That's fine. It will try to find the post-fit taps all the same. If they aren't available (they are generated by the Fitter), then you'll need to let the compile finish, set your netlist type to Post Fit, and recompile once more.
I wonder if the Nios II plugin is creating post-fit taps when it really needs to create pre-synthesis taps. Look in your QSF for the nodes you tapped with the Nios II plugin. You should see them referenced in assignments that look like:
POST_FIT_CONNECT_TO_SLD_NODE_ENTITY_PORT (post-fit tap)
CONNECT_TO_SLD_NODE_ENTITY_PORT (pre-synthesis tap)
Josh