I fixed it, thanks to some guy on a discord im in. Basically, you have to edit the user.pso2 file under Documents\SEGA and navigate to your PSO2 version (NA or NA_STEAM) and scroll down that file to Windows.
Basically, edit the Height3d, Width3d, Height and Width values to whatever monitor size your gaming monitor is on (mine is 1440p, so 1440, 2560, 1440 and 2560. Entering in those values manually fixed it. (Also try to adjust DisplayNo to either 0, 1 or 2. 0 = 1, 1=2, 2=3)
Not sure why the Steam version is the only one that messed with a multi-monitor setup like mine (was fine on both JPN and MS versions), but that fixed it for me regardless.