diff -up parted-1.9.0/libparted/disk.c.entiredisk parted-1.9.0/libparted/disk.c
--- parted-1.9.0/libparted/disk.c.entiredisk	2009-12-15 19:22:01.000000000 +0100
+++ parted-1.9.0/libparted/disk.c	2009-12-15 20:19:30.000000000 +0100
@@ -785,10 +785,15 @@ ped_disk_max_partition_start_sector (con
 int
 ped_disk_set_flag(PedDisk *disk, PedDiskFlag flag, int state)
 {
+        int ret;
+
         PED_ASSERT (disk != NULL, return 0);
 
         PedDiskOps *ops = disk->type->ops;
 
+        if (!_disk_push_update_mode(disk))
+                return 0;
+
         if (!ped_disk_is_flag_available(disk, flag)) {
                 ped_exception_throw (
                         PED_EXCEPTION_ERROR,
@@ -796,10 +801,16 @@ ped_disk_set_flag(PedDisk *disk, PedDisk
                         "The flag '%s' is not available for %s disk labels.",
                         ped_disk_flag_get_name(flag),
                         disk->type->name);
+                _disk_pop_update_mode(disk);
                 return 0;
         }
 
-        return ops->disk_set_flag(disk, flag, state);
+        ret = ops->disk_set_flag(disk, flag, state);
+
+        if (!_disk_pop_update_mode (disk))
+                return 0;
+
+        return ret;
 }
 
 /**
diff -up parted-1.9.0/libparted/labels/dos.c.entiredisk parted-1.9.0/libparted/labels/dos.c
--- parted-1.9.0/libparted/labels/dos.c.entiredisk	2009-12-15 19:22:01.000000000 +0100
+++ parted-1.9.0/libparted/labels/dos.c	2009-12-15 20:19:38.000000000 +0100
@@ -2242,7 +2242,10 @@ add_startend_metadata (PedDisk* disk)
 	else
 		init_end = PED_MIN (dev->bios_geom.sectors - 1, init_end - 1);
 
-	if (!get_end_last_nonfree_part(disk, &final_start))
+        DosDiskData *disk_specific = disk->disk_specific;
+        if (!disk_specific->cylinder_alignment)
+                final_start = dev->length - 1;
+        else if (!get_end_last_nonfree_part(disk, &final_start))
 		final_start = ped_round_down_to (dev->length, cyl_size);
 	else
 		final_start = PED_MAX (final_start + 1,