Yeah, I tried Alt+Enter and it doesn't do anything when running through WinEQ, the screen blinks like it thinks it changed but actually doesn't.
I actually got it working another way so this might work for someone else. I found the Duxa's All in One installer tool here
http://p99.yourfirefly.com/ & ran that so now if I run the game through the EQemu launcher shortcut it will run fullscreen.
However it seems there was an oversight by whoever wrote the installer program. When you select your choices and it asks you if you want windowed or full screen etc and which resolution. The choice for 1080p is written as 1900x1000 instead of 1920x1080. So initially if I tried to go full screen it would just crash the game. Once I realized the mistake I edited my eq.ini config file and changed all the values to 1920 x 1080 instead and now everything seems to work fine, I can Alt+Enter to toggle full screen and it works no problem. Like I said though I do have to start through the EQemu launcher though, if I start through WinEQ I still have the same issue with going full screen. From what I understand though the Duxa's Installer solves all the same issues that WinEQ does, is that right? If so then all should be good for me at this point.