Videorate calculates it's next_ts as : 

videorate->next_ts = videorate->segment.accum + videorate->segment.start +
        gst_util_uint64_scale (videorate->out,
        videorate->to_rate_denominator * GST_SECOND,
        videorate->to_rate_numerator);

But ->out (the number if frames outputed) is not reset when a newsegment is received thus if a second newsegment is received, next ts will be in the future of  
it's previous stream time relative to the new newsegment start.

  So if a stream played 30 frames a 30 frames per sec already.. and the new newsegmetn is starting at Sec 5.. rather then start at sec 5.. it will start a sec 6 .. When it should start at the newsegment start...

The next_ts should also be reset when receiving a newsegment so that it starts at segment.start + segment.accum... (since intime is calculated as ts + segment.accum)

Here's a patch to fix this issue...