diff --git a/src/finalize.F90 b/src/finalize.F90
index 76ae8dc9a5..8f9bb40eb3 100644
--- a/src/finalize.F90
+++ b/src/finalize.F90
@@ -27,7 +27,7 @@ contains
 
     ! show timing statistics
     call timer_stop(time_total)
-    if (master) call print_runtime()
+    if (master .and. (.not. plotting)) call print_runtime()
 
 #ifdef HDF5
     if (master) then
diff --git a/src/geometry.F90 b/src/geometry.F90
index 31b40045a2..efcfe45ac2 100644
--- a/src/geometry.F90
+++ b/src/geometry.F90
@@ -124,7 +124,9 @@ contains
        ! select cells based on whether we are searching a universe or a provided
        ! list of cells (this would be for lists of neighbor cells)
        if (use_search_cells) then
-          index_cell = search_cells(i) 
+          index_cell = search_cells(i)
+          ! check to make sure search cell is in same universe
+          if (cells(index_cell) % universe /= p % coord % universe) cycle
        else
           index_cell = univ % cells(i)
        end if
diff --git a/src/initialize.F90 b/src/initialize.F90
index d7791fc932..acb585c192 100644
--- a/src/initialize.F90
+++ b/src/initialize.F90
@@ -313,27 +313,27 @@ contains
     ! We also need to allocate the cell count lists for each universe. The logic
     ! for this is a little more convoluted. In universe_dict, the (key,value)
     ! pairs are the id of the universe and the index in the array. In
-    ! ucount_dict, it's the id of the universe and the number of cells.
+    ! cells_in_univ_dict, it's the id of the universe and the number of cells.
 
     key_list => dict_keys(universe_dict)
     do while (associated(key_list))
        ! find index of universe in universes array
-       i_univ = key_list%data%value
+       i_univ = key_list % data % value
        univ => universes(i_univ)
-       univ % id = key_list%data%key
+       univ % id = key_list % data % key
 
        ! check for lowest level universe
        if (univ % id == 0) BASE_UNIVERSE = i_univ
        
        ! find cell count for this universe
-       n_cells_in_univ = dict_get_key(cells_in_univ_dict, key_list%data%key)
+       n_cells_in_univ = dict_get_key(cells_in_univ_dict, univ % id)
 
        ! allocate cell list for universe
        allocate(univ % cells(n_cells_in_univ))
        univ % n_cells = n_cells_in_univ
        
        ! move to next universe
-       key_list => key_list%next
+       key_list => key_list % next
     end do
 
     ! Also allocate a list for keeping track of where cells have been assigned
diff --git a/src/output.F90 b/src/output.F90
index 4acbf169a2..0bcd7bd579 100644
--- a/src/output.F90
+++ b/src/output.F90
@@ -6,7 +6,7 @@ module output
   use constants
   use datatypes,       only: dict_get_key
   use endf,            only: reaction_name
-  use geometry_header, only: Cell, Universe, Surface
+  use geometry_header, only: Cell, Universe, Surface, BASE_UNIVERSE
   use global
   use mesh_header,     only: StructuredMesh
   use particle_header, only: Particle, LocalCoord
@@ -260,8 +260,8 @@ contains
 
     ! Print surface
     if (p % surface /= NONE) then
-       s => surfaces(p % surface)
-       write(ou,*) '  Surface = ' // to_str(s % id)
+       s => surfaces(abs(p % surface))
+       write(ou,*) '  Surface = ' // to_str(sign(s % id, p % surface))
     end if
 
     write(ou,*) '  Weight = ' // to_str(p % wgt)
@@ -370,6 +370,7 @@ contains
     integer :: unit_
     character(MAX_LINE_LEN) :: string
     type(Cell), pointer     :: c => null()
+    type(Universe), pointer :: base_u
 
     if (present(unit)) then
        unit_ = unit
@@ -377,7 +378,12 @@ contains
        unit_ = OUTPUT_UNIT
     end if
 
+    base_u => universes(BASE_UNIVERSE)
+
     write(unit_,*) 'Universe ' // to_str(univ % id)
+    if (associated(univ, base_u)) then
+       write(unit_,*) '   Base Universe'
+    end if
     write(unit_,*) '    Level = ' // to_str(univ % level)
     string = ""
     do i = 1, univ % n_cells
diff --git a/src/plot.F90 b/src/plot.F90
index 77ae883c03..673e8946e8 100644
--- a/src/plot.F90
+++ b/src/plot.F90
@@ -170,7 +170,7 @@ contains
 
              ! Since boundary conditions are disabled in plotting mode, we need
              ! to manually add the last segment
-             if (surfaces(abs(surface_crossed)) % bc == BC_VACUUM) then
+             if (surfaces(abs(surface_crossed)) % bc /= BC_TRANSMIT) then
                 p % coord0 % xyz(1) = last_x_coord
                 write(UNIT=UNIT_PLOT) p % coord0 % xyz, 0
                 exit