Hi,
So the issue is not seen if you always return GST_PAD_PROBE_OK in filtering_probe()? Not sure if it is related but we have seen an issue about adding prob functions:
Doesn't work nvv4l2decoder in deep-stream-python-apps - #11 by DaneLLL
Another suspicion is about synchronization mechanism in gstreamer. If you return GST_PAD_PROBE_DROP irregularly, the downstream elements receive buffers with random-interval timestamps, and may trigger the issue. Please set sync=false to the two multifilesink and try again.