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The term brings the following up:

ZZogl: creating zerogs
ZZogl: Got Doublebuffered Visual!
ZZogl: glX-Version 1.2
Xlib: extension "XFree86-VidModeExtension" missing on display "/tmp/launch-mZI88i/:0".
ZZogl: Depth 24
ZZogl: you have Direct Rendering!
ZZogl: Using multitexturing
ZZogl: Maximun texture size is 2048 for Tex_2d and 2048 for Tex_NV
ZZogl: Disabling MRT depth writing
ZZogl: Disabling MRT depth writing

Then it pops up a blank window with 'ZeroGS' along the top bar. Help?

Maybe uncompatible game? What game was it? And you videocard is not very good for ZZogl.

The game is Radiata Stories, but even when I boot just the bios that happens so I don't think it's that.

Old ZZogl versions have a ton of issues with RS. Newer ones have a bunch to, but at least skipdraw could avoid some.

Ok, well how would I fix my issue then?

Build a newer ZZogl by yourself. It's the only one way. Or wait until somebody do it for you.