diff --git a/gnuradio-core/src/lib/runtime/gr_flat_flowgraph.cc b/gnuradio-core/src/lib/runtime/gr_flat_flowgraph.cc
index e97fa13..adb1f56 100644
--- a/gnuradio-core/src/lib/runtime/gr_flat_flowgraph.cc
+++ b/gnuradio-core/src/lib/runtime/gr_flat_flowgraph.cc
@@ -63,8 +63,13 @@ gr_flat_flowgraph::setup_connections()
     cast_to_block_sptr(*p)->set_detail(allocate_block_detail(*p));
 
   // Connect inputs to outputs for each block
-  for(gr_basic_block_viter_t p = blocks.begin(); p != blocks.end(); p++)
+  for(gr_basic_block_viter_t p = blocks.begin(); p != blocks.end(); p++) {
     connect_block_inputs(*p);
+
+    gr_block_sptr block = cast_to_block_sptr(*p);   
+    setup_buffer_alignment(block);
+  }
+
 }
 
 gr_block_detail_sptr
@@ -245,27 +250,8 @@ gr_flat_flowgraph::merge_connections(gr_flat_flowgraph_sptr old_ffg)
 	std::cout << "new block" << std::endl;
       connect_block_inputs(block);
 
-      const int alignment = volk_get_alignment();
-      for(int i = 0; i < block->detail()->ninputs(); i++) {
-	void *r = (void*)block->detail()->input(i)->read_pointer();
-	unsigned long int ri = (unsigned long int)r % alignment;
-	if(ri != 0) {
-	  size_t itemsize = block->detail()->input(i)->get_sizeof_item();
-	  block->detail()->input(i)->update_read_pointer(ri/itemsize);
-	  block->set_unaligned(0);
-	  block->set_is_unaligned(false);
-	}
-      }
-      for(int i = 0; i < block->detail()->noutputs(); i++) {
-	void *w = (void*)block->detail()->output(i)->write_pointer();
-	unsigned long int wi = (unsigned long int)w % alignment;
-	if(wi != 0) {
-	  size_t itemsize = block->detail()->output(i)->get_sizeof_item();
-	  block->detail()->output(i)->update_write_pointer(wi/itemsize);
-	  block->set_unaligned(0);
-	  block->set_is_unaligned(false);
-	}
-      }
+      // Make sure all buffers are aligned
+      setup_buffer_alignment(block);
     }
 
     // Now deal with the fact that the block details might have changed numbers of 
@@ -273,6 +259,35 @@ gr_flat_flowgraph::merge_connections(gr_flat_flowgraph_sptr old_ffg)
   }  
 }
 
+void
+gr_flat_flowgraph::setup_buffer_alignment(gr_block_sptr block)
+{
+  const int alignment = volk_get_alignment();
+  for(int i = 0; i < block->detail()->ninputs(); i++) {
+    void *r = (void*)block->detail()->input(i)->read_pointer();
+    unsigned long int ri = (unsigned long int)r % alignment;
+    //std::cout << "reader: " << r << "  alignment: " << ri << std::endl;
+    if(ri != 0) {
+      size_t itemsize = block->detail()->input(i)->get_sizeof_item();
+      block->detail()->input(i)->update_read_pointer(ri/itemsize);
+    }
+    block->set_unaligned(0);
+    block->set_is_unaligned(false);
+  }
+
+  for(int i = 0; i < block->detail()->noutputs(); i++) {
+    void *w = (void*)block->detail()->output(i)->write_pointer();
+    unsigned long int wi = (unsigned long int)w % alignment;
+    size_t itemsize = block->detail()->output(i)->get_sizeof_item();
+    //std::cout << "writer: " << w << "  alignment: " << wi << std::endl;
+    if(wi != 0) {
+      block->detail()->output(i)->update_write_pointer(wi/itemsize);
+    }
+    block->set_unaligned(0);
+    block->set_is_unaligned(false);
+  }
+}
+
 void gr_flat_flowgraph::dump()
 {
   for (gr_edge_viter_t e = d_edges.begin(); e != d_edges.end(); e++)
diff --git a/gnuradio-core/src/lib/runtime/gr_flat_flowgraph.h b/gnuradio-core/src/lib/runtime/gr_flat_flowgraph.h
index 2cc8836..ce86350 100644
--- a/gnuradio-core/src/lib/runtime/gr_flat_flowgraph.h
+++ b/gnuradio-core/src/lib/runtime/gr_flat_flowgraph.h
@@ -63,6 +63,15 @@ private:
   gr_block_detail_sptr allocate_block_detail(gr_basic_block_sptr block);
   gr_buffer_sptr allocate_buffer(gr_basic_block_sptr block, int port);
   void connect_block_inputs(gr_basic_block_sptr block);
+
+  /* When reusing a flowgraph's blocks, this call makes sure all of the 
+   * buffer's are aligned at the machine's alignment boundary and tells
+   * the blocks that they are aligned.
+   *
+   * Called from both setup_connections and merge_connections for
+   * start and restarts.
+   */
+  void setup_buffer_alignment(gr_block_sptr block);
 };
 
 #endif /* INCLUDED_GR_FLAT_FLOWGRAPH_H */