Can you help me understand this a little further? I do have IPv6 enabled. I assume you're saying normally this isn't an issue because EQ runs on IPv4 so with normal port mirroring this isn't an issue? (I'm a little ignorant on this- apologies).
Exactly. When SEQ does its own capture, it filters out ipv6, so it isn't an issue in normal usage. But playback of an existing capture uses different code that doesn't filter ipv6. So to play back a manual capture (from tcpdump/wireshark) in SEQ, you need to make sure that the capture doesn't contain ipv6 otherwise you're likely to have problems. But normal play should be fine.

Playback should be straightforward. If you run showeq with --help, it will give you what you need. But it's something like --playback-tcpdump-filename=/path/to/capture/file and --playback-speed=N where N is how fast to play back. Then if it's too fast/slow, you can adjust speed in the program from one of the menus (file menu I think?) or using ctrl-z/ctrl-x.