Comparing frames is fairly difficult.
I posted some Wireshark information with the difficulties and some Comm View (I use Comm View) that could be a little more hopeful.
Compare Wireshark frames
That actually sounds like a fun little project if it doesn't exist.
You might be able to use the perl NET::PCAP library to ingest the
file, then make the necessary comparison at the offset you desire. You
could render the differences and frame numbers into html. I wish I had
more time (and PERL knowledge) so I could give you more direction.
Maybe someone else knows of something already built (or something that
could be easily adapted).
I don't know all of your specifics, but maybe a dissector could be
written for the industrial protocol you are analyzing and do away with
the need to compare.
Compare frames in Comm View
Damaged frames are not counted in other charts and tables for the
obvious reason: No part of a frame with the wrong CRC value is
credible. It may have a completely wrong IP address, data payload,
etc., although in real life such frames bear a resemblance to the
original. For the same reason CRC Errors cannot be attributed to a
particular wireless AP or station, as it's impossible to determine the
real sender's MAC address.
Nevertheless, the user may want to check the Capture damaged frames
box in the options, in which case damaged frames will also be shown in
the packet list. By default, such frames are marked with red and have
the "CRC" identifier shown in the Errors column of the Packets tab
Not all the wireless adapters are capable of passing damaged frames to
the application level. Such functionality is guaranteed only for the
recommended adapters supported by CommView for WiFi.