@mhertzfeld:
You are not alone, I see the same thing in my setup.
I had asked a similar question a few months back but never got an answer.
https://forum.pfsense.org/index.php?topic=113631.0
I am thinking this has something to do with it.
https://en.wikipedia.org/wiki/Promiscuous_mode
Are the pfsense and snort versions the same on the system you see the vlan traffic in LAN and the system you don't?
Promiscuous mode would make sense, but I thought previously Snort was putting the interfaces into promiscuous mode as well, even though it wasn't seeing all the traffic. I actually changed my configuration to adjust for this, so I was surprised to see it working as expected on the new system.
I have one system available to test on, it is fully up to date (pfSense and Snort) and it is behaving as described above, running Snort on the physical interface alerts on traffic for the VLANs on that interface as well. I know that this was not the case previously, but that was probably on 2.2.6 and with a previous version of Snort.