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Is this a problem with libpcap?
Unlikely - on Linux (and most other platforms), libpcap doesn't time-stamp the packets, the OS networking stack or the OS capture mechanism, in kernel mode, time-stamps the packets.
Probably either 1) the packets really are getting delayed in getting to the receiver or 2) there's a delay between the arrival of the packet on the receiver's network adapter and a time stamp being applied to it by the Linux networking stack.
BTW, in what fashion is ARP involved here?
