I've never had any real issues with H264 or MPEG2 timestamps, they usually are rather consistent. (VC-1 is another matter, different splitters give different results, but there are luckily only 2 ways they do it)
If you just look at the incoming timestamps, they will of course be out of order, because those are presentation timestamps. They belong to the frame they are attached to, and frames are delivered in decode order, not in presentation order.
Any specific clip that gives you trouble?
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LAV Filters - open source ffmpeg based media splitter and decoders
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