Please provide a backtrace - not reproduceable.

It do not crash now with current CVS. But it still do not play and on the
console I get the following:
(totem:31366): GStreamer-WARNING **: element internal_thread claimed
state-change success,but state didn't change to PLAYING. State is PAUSED
(NONE_PENDING pending), fix the element

It might be using another mod player for you than for me (since we have 2).
Which one does it use? Can you attach a --gst-debug=decodebin:5 log?

I only have modplug installed. I get mikmod going and re-test with that.

Ok, tried removing the modplug plugin. When running just 'totem amiga.mod' totem
segfaults. When running with --gst-debug then it sometimes crash and sometime
give me an error message saying that it failed to play; reason unknown.
Attaching both tracefile for the segfault and a log file for the reason unknown
problem.

With modplug I am getting the error 
(totem:14983): GStreamer-WARNING **: element internal_thread claimed
state-change success,but state didn't change to PLAYING. State is PAUSED
(NONE_PENDING pending), fix the element when just running plainly and a 'failed
to play;reason unknown' popping up in the console.
Same when with debug on, attaching log for that.

Created attachment 34396 [details]
mikmod crash trace

Created attachment 34397 [details]
mikmod debug output

Created attachment 34398 [details]
modplug debug output

Reopening this as I provided lots of debug files

You're saying that mikmod segfaults. The line number that you give is an
g_assert(), though. Are you sure it didn't crash on a failed assertion? Please
be very accurate on those things, they make a large difference.

Mikmod don't segfault anymore, doesn't play either just spews out a lot of:
(totem:13978): GStreamer-WARNING **: element internal_thread claimed
state-change success,but state didn't change to PLAYING. State is PAUSED
(NONE_PENDING pending), fix the element

So it seems modplug and mikmod are giving me the identical behaviour now.

Current CVS gives me this behaviour:

[cschalle@cschalle small]$ gst-launch playbin
uri=file:///home/cschalle/media/small/amiga.mod
RUNNING pipeline ...

** (process:23959): WARNING **: could not link audio/x-raw-int,
signed=(boolean)false, width=(int)8, depth=(int)8, rate=(int)44100, channels=(int)2
Waiting for the state change...

That was a mistake of mine in gst-ffmpeg, fixed in CVS. Please try again.

I think I've fixed the initial bug, too. The problem (...) was that modplug has
various allowed caps, and we were renegotiating inside the chain function, when
a format has already been selected. That caused invalid fixation. I've fixed
that by narrowing down allowed caps when renegotiating from within the chain
function in the stream selector. With that change, I can no longer reproduce it.
Please reopen if you still see it.