Looking at the trace you provided, I am mostly seeing correct every-other ack behavior. I continue to wonder if the bad pcap trace is masking something else. Try setting net.bpf.maxbufsize larger, but I am still not used to seeing 0-len captures even if packets are dropped. In counting packets, I concur that something seems wrong. But I am unable to find much fine-grained oddness. Big buffers should not be an issue.
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