I am also experiencing this. My best guess is that Arpwatch is starting itself at boot, then pfSense is starting Arpwatch again after that (or pfSense starts it first? I'm not sure).

In addition to what others have mentioned, I have noticed these facts:

1) After installing Arpwatch everything works fine, there is one instance of Arpwatch running per configured interface.

2) After a reboot, trouble starts, two instances of Arpwatch running per interface.

3) After configuring Arpwatch, if you disable it in the pfSense webconfigurator, and then reboot, Arpwatch works as expected, one instance running per interface, no repeat emails for existing hosts, you can view the database from the webconfigurator and it does get updated by Arpwatch. The only downside to this is that it doesn't show up in the pfSense webconfigurator as a running service, but it is in fact running and working correctly at this point.

I would suggest to others in the meantime to install and configure Arpwatch from the webconfigurator, then uncheck "Enable Arpwatch", click save, and reboot. That is the state my system is in at this point, I will report here if I see any issues arise from running it this way. I would also suggest anyone doing this keep an eye on this thread, because when this issue gets fixed you'll need to enable Arpwatch again in the webconfigurator.