Appion

creating a new stack based on an xmipp "sortJunkStack.py" stack (using the "Stacks:" option instead of "Particles:" option in makestack2) creates a stack of particles that are not in the same order as the xmipp sorted stack. The resulting stack is not in the same order as the original unsorted stack either. Any substacks created using this xmipp sorted stack get the correct stack particles, but going back and re-stacking with makestack2 doesn't work properly. So I think somehow the stack particles are being tracked correctly, but not the original particle entries in the database.
Sorry if this bug description is really convoluted, I can try to further clarify if necessary.