Testpipeline:
gst-lauch -v filesrc location=test.mpg ! mpegpsdemux ! h264parse ! fakesink

misses to set the buffer flags


/GstPipeline:pipeline0/GstFakeSink:fakesink0: last-message = "chain   ******* (fakesink0:sink) (53089 bytes, timestamp: 0:00:03.420033333, duration: none, offset: -1, offset_end: -1, flags: 1 ro ) 0xbca78"
/GstPipeline:pipeline0/GstFakeSink:fakesink0: last-message = "chain   ******* (fakesink0:sink) (41399 bytes, timestamp: 0:00:03.453400000, duration: none, offset: -1, offset_end: -1, flags: 1 ro ) 0xbcd48"
/
.....and endlesss 'flags: 1'....

A quick fix (just for testing) is the following patch:

diff --git a/gst/videoparsers/gsth264parse.c b/gst/videoparsers/gsth264parse.c
index cf81657..9dd8b51 100644
--- a/gst/videoparsers/gsth264parse.c
+++ b/gst/videoparsers/gsth264parse.c
@@ -1656,7 +1656,7 @@ gst_h264_parse_set_caps (GstBaseParse * parse, GstCaps * caps)
   }
 
   if (format == h264parse->format && align == h264parse->align) {
-    gst_base_parse_set_passthrough (parse, TRUE);
+    gst_base_parse_set_passthrough (parse, FALSE);
 
     /* we did parse codec-data and might supplement src caps */
     gst_h264_parse_update_src_caps (h264parse, caps);

Output with patch applied:

/GstPipeline:pipeline0/GstFakeSink:fakesink0: last-message = "chain   ******* (fakesink0:sink) (62658 bytes, timestamp: 0:00:05.805711111, duration: none, offset: 7351588, offset_end: -1, flags: 257 ro delta_unit ) 0xbcc78"
/GstPipeline:pipeline0/GstFakeSink:fakesink0: last-message = "chain   ******* (fakesink0:sink) (46709 bytes, timestamp: 0:00:05.839066666, duration: none, offset: 7414246, offset_end: -1, flags: 257 ro delta_unit ) 0xbcce0"
/GstPipeline:pipeline0/GstFakeSink:fakesink0: last-message = "chain   ******* (fakesink0:sink) (131011 bytes, timestamp: 0:00:05.872433333, duration: none, offset: 7460955, offset_end: -1, flags: 0 ) 0xbcdb0"
/GstPipeline:pipeline0/GstFakeSink:fakesink0: last-message = "chain   ******* (fakesink0:sink) (52341 bytes, timestamp: 0:00:05.922477777, duration: none, offset: 7591966, offset_end: -1, flags: 257 ro delta_unit ) 0xbcd48"
/GstPipeline:pipeline0/GstFakeSink:fakesink0: last-message = "chain   ******* (fakesink0:sink) (37758 bytes, timestamp: 0:00:05.955855555, duration: none, offset: 7644307, offset_end: -1, flags: 257 ro delta_unit ) 0xbcc10"


I think the problem was introduced by the following commit: 
http://cgit.freedesktop.org/gstreamer/gst-plugins-bad/commit/gst/videoparsers/gsth264parse.c?id=6a8d66728f0c88c4e087d489084ecc31071dc251

As fix for:
https://bugzilla.gnome.org/show_bug.cgi?id=650228

I think the fakesink element accept the new caps and as consequence the h264parse is disabled by the gst_base_parse_set_passthrough (parse, TRUE); call......