Different image sources provide images with different pixels at the origin. The attached patch adds a parameter to the bayer plugin, that allows to support them all.

Other information:
Index: gst/bayer/gstbayer2rgb.c
===================================================================
RCS file: /cvs/gstreamer/gst-plugins-bad/gst/bayer/gstbayer2rgb.c,v
retrieving revision 1.6
diff -u -r1.6 gstbayer2rgb.c
--- gst/bayer/gstbayer2rgb.c	12 Jun 2008 14:49:15 -0000	1.6
+++ gst/bayer/gstbayer2rgb.c	19 Nov 2008 11:04:17 -0000
@@ -96,6 +96,18 @@
 
 typedef void (*GstBayer2RGBProcessFunc) (GstBayer2RGB *, guint8 *, guint);
 
+/*
+ * We define values for the colors, just to make the code more readable.
+ */
+typedef enum
+{
+  RED,		               /* Pure red element */
+  GREENB,	               /* Green element which is on a blue line */
+  BLUE,		               /* Pure blue element */ 
+  GREENR,	               /* Green element which is on a red line */
+  GST_BAYER_START_PIXEL_COLOUR_DEFAULT = GREENB,
+} GstBayerStartPixelColour;
+
 struct _GstBayer2RGB
 {
   GstBaseTransform basetransform;
@@ -108,6 +120,8 @@
   int r_off;                    /* offset for red */
   int g_off;                    /* offset for green */
   int b_off;                    /* offset for blue */
+
+  GstBayerStartPixelColour start_colour;
 };
 
 struct _GstBayer2RGBClass
@@ -138,7 +152,8 @@
 
 enum
 {
-  PROP_0
+  PROP_0,
+  PROP_BAYER_START_PIXEL_COLOUR,
 };
 
 #define DEBUG_INIT(bla) \
@@ -178,6 +193,26 @@
           gst_caps_from_string (SINK_CAPS)));
 }
 
+#define GST_BAYER_START_PIXEL_COLOUR (gst_bayer_start_pixel_colour_get_type ())
+static GType
+gst_bayer_start_pixel_colour_get_type (void)
+{
+  static GType start_pixel_colour_type;
+  static const GEnumValue colour_types[] = {
+    {RED,	"Red",		"red"},
+    {BLUE,	"Blue",		"blue"},
+    {GREENR,	"Green-Red",	"green_red"},
+    {GREENB,	"Green-Blue",	"green_blue"},
+    {0,		NULL,		NULL}
+  };
+
+  if (!start_pixel_colour_type)
+    start_pixel_colour_type =
+        g_enum_register_static ("GstBayerStartPixelColour", colour_types);
+
+  return start_pixel_colour_type;
+}
+
 static void
 gst_bayer2rgb_class_init (GstBayer2RGBClass * klass)
 {
@@ -195,6 +230,11 @@
       GST_DEBUG_FUNCPTR (gst_bayer2rgb_set_caps);
   GST_BASE_TRANSFORM_CLASS (klass)->transform =
       GST_DEBUG_FUNCPTR (gst_bayer2rgb_transform);
+
+  g_object_class_install_property (gobject_class, PROP_BAYER_START_PIXEL_COLOUR,
+      g_param_spec_enum ("start_pixel", "B/R/GB/GR first", "Colour of the start pixel",
+          GST_BAYER_START_PIXEL_COLOUR, GST_BAYER_START_PIXEL_COLOUR_DEFAULT,
+          G_PARAM_READWRITE));
 }
 
 static void
@@ -209,8 +249,12 @@
 gst_bayer2rgb_set_property (GObject * object, guint prop_id,
     const GValue * value, GParamSpec * pspec)
 {
+  GstBayer2RGB *filter = GST_BAYER2RGB (object);
 
   switch (prop_id) {
+    case PROP_BAYER_START_PIXEL_COLOUR:
+      filter->start_colour = g_value_get_enum (value);
+      break;
     default:
       G_OBJECT_WARN_INVALID_PROPERTY_ID (object, prop_id, pspec);
       break;
@@ -221,8 +265,12 @@
 gst_bayer2rgb_get_property (GObject * object, guint prop_id,
     GValue * value, GParamSpec * pspec)
 {
+  GstBayer2RGB *filter = GST_BAYER2RGB (object);
 
   switch (prop_id) {
+    case PROP_BAYER_START_PIXEL_COLOUR:
+      g_value_set_enum (value, filter->start_colour);
+      break;
     default:
       G_OBJECT_WARN_INVALID_PROPERTY_ID (object, prop_id, pspec);
       break;
@@ -289,6 +337,7 @@
   filter->r_off = 0;
   filter->g_off = 0;
   filter->b_off = 0;
+  filter->start_colour = GST_BAYER_START_PIXEL_COLOUR_DEFAULT;
 }
 
 static GstCaps *
@@ -356,14 +405,6 @@
   return FALSE;
 }
 
-/*
- * We define values for the colors, just to make the code more readable.
- */
-#define	RED	0               /* Pure red element */
-#define	GREENB	1               /* Green element which is on a blue line */
-#define	BLUE	2               /* Pure blue element */
-#define	GREENR	3               /* Green element which is on a red line */
-
 /* Routine to generate the top and bottom edges (not including corners) */
 static void
 hborder (uint8_t * input, uint8_t * output, int bot_top,
@@ -463,23 +504,40 @@
 static void
 do_row0_col0 (uint8_t * input, uint8_t * output, GstBayer2RGB * filter)
 {
-  int type;
+  GstBayerStartPixelColour type_top, type_bottom, type_left, type_right;
+
+  type_top = filter->start_colour;
+
+  switch (filter->start_colour) {
+    case RED:
+      type_bottom = filter->height & 1 ? type_top : GREENB;
+      type_left = BLUE;
+      type_right = filter->width & 1 ? type_left : GREENB;
+      break;
+    case BLUE:
+      type_bottom = filter->height & 1 ? type_top : GREENR;;
+      type_left = RED;
+      type_right = filter->width & 1 ? type_left : GREENR;
+      break;
+    case GREENR:
+      type_bottom = filter->height & 1 ? type_top : BLUE;;
+      type_left = GREENB;
+      type_right = filter->width & 1 ? type_left : BLUE;
+      break;
+    case GREENB:
+      type_bottom = filter->height & 1 ? type_top : RED;
+      type_left = GREENR;
+      type_right = filter->width & 1 ? type_left : RED;
+      break;
+  }
 
   /* Horizontal edges */
-  hborder (input, output, 0, GREENB, filter);
-  if (filter->height & 1)
-    type = GREENB;              /* odd # rows, "bottom" edge same as top */
-  else
-    type = RED;                 /* even #, bottom side different */
-  hborder (input, output, 1, type, filter);
+  hborder (input, output, 0, type_top, filter);
+  hborder (input, output, 1, type_bottom, filter);
 
   /* Vertical edges */
-  vborder (input, output, 0, GREENR, filter);
-  if (filter->width & 1)
-    type = GREENR;              /* odd # cols, "right" edge same as left */
-  else
-    type = RED;                 /* even #, right side different */
-  vborder (input, output, 1, type, filter);
+  vborder (input, output, 0, type_left, filter);
+  vborder (input, output, 1, type_right, filter);
 }
 
 static void
@@ -542,9 +600,9 @@
 static void
 do_body (uint8_t * input, uint8_t * output, GstBayer2RGB * filter)
 {
-  int ip, op;                   /* input and output pointers */
-  int w, h;                     /* loop indices */
-  int type;                     /* calculated colour of current element */
+  int ip, op;                    /* input and output pointers */
+  int w, h;                      /* loop indices */
+  GstBayerStartPixelColour type; /* calculated colour of current element */
   int a1, a2;
   int v1, v2, h1, h2;
 
@@ -562,10 +620,24 @@
      * the pixel at position (1,1).  Assuming BG format, this should
      * be RED for odd-numbered rows and GREENB for even rows.
      */
-    if (h & 1)
-      type = RED;
-    else
-      type = GREENB;
+
+    type = filter->start_colour;
+
+    switch (filter->start_colour) {
+      case RED:
+        type = h & 1 ? GREENB : RED;
+	break;
+      case BLUE:
+        type = h & 1 ? GREENR : BLUE;
+        break;
+      case GREENR:
+        type = h & 1 ? BLUE : GREENR;
+        break;
+      case GREENB:
+        type = h & 1 ? RED : GREENB;
+        break;
+    }
+
     /* Calculate the starting position for the row */
     op = h * filter->width * filter->pixsize;   /* output (converted) pos */
     ip = h * filter->stride;    /* input (bayer data) pos */