There's a command you can run, winecfg, which lets you configure WINE. You can set which version of Windows it's trying to emulate, whether it runs EQ in a virtual desktop, etc.
I'd recommend playing around with the Windows versions, and with the options in the Graphics tab (eg. that virtual desktop thing I mentioned), and see if different configurations help. I can't say specifically "use Windows 95, it will fix things", but very often trying different configurations will help.
Also, if you haven't already, make sure you're using the latest graphics drivers ... or at least the latest available for your repo (eg. on Debian/Ubuntu/Mint the latest ones in apt-get).
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