@rumblpak I am using a Cisco Layer 3 Switch (4506E) with different EAP connected, however, the concept should be the same.

If I understand what you have listed, it is roughly the same as I have.  I am not using VLAN 1 as default.  I use VLAN 254. In my case, I have the native VLAN set to 254, which is untagged, and all other VLANS tagged, and it works correctly.  You can see the port config below:

interface GigabitEthernet2/6
 description Lobby AP
 switchport trunk native vlan 254
 switchport trunk allowed vlan 25,100-102,112,113,200,254
 switchport mode trunk
 logging event link-status

My EAP's don't use VLAN 254 for ANY of the SSID's though, so for a test, you may want to try not using VLAN 1, and just use another VLAN for your traffic and tag it as well.  At least as a test.  To be clear though, I do use VLAN 254 as the management VLAN, just not on any tagged SSID's.   Hopefully that make sense.

If that doesn't work, make sure that there are no firewall rules, etc that could be blocking traffic.

  @rumblpak yeah, that is weird.  Can you ping your plex server?  Or any other device on the network?  Can you ping the gateway for those VLAN's?

  @rumblpak i know this is probably a stupid question, but in addition to the above, make sure you didn't mark the SSID's as a 'guest' network.

  @muzicman0 

ICMP traffic (ping) works fine, its only udp and tcp traffic where I see issues. The main SSID does not have guest enabled but the other two do, would that be a problem?

  @rumblpak  yes, that's the problem. Guest networks will block any traffic that isn't destined for the wan. So any local ip's will be blocked (ie:192.168.0.0/16). 

Uncheck guest on those and use acl's to block traffic that you want between vlans. 

Edit: replied from my phone, so please excuse any typos!

  @muzicman0 even on the network that isn't a guest network?

  @rumblpak if client and server are on the same vlan and same subnet, and it isn't a guest network then it should work. If either guest or client are on guest then it won't work. 

  @rumblpak no idea at this point. I think it would be worth it to try disabling the guest on all ssid's just as a test. In theory it shouldn't matter, but perhaps there is a bug or something. It might even be worth rebooting everything after making that change.