If it's an NVIDIA card, the recent drivers have been having tons of issues lately. It's not rendering full screen applications correctly, so you might need to try an older driver like 182.50 or something. If you have an ATi card, well, I'm not sure as I don't have one.
You can try this, however.
Go into your eqclient.ini file and do the following.
1.) Find the [Video Modes] section. Edit it to the following if it isn't already.
[VideoMode]
Width=1680
Height=1050
WidthWindowed=1680
HeightWindowed=1050
FullscreenRefreshRate=0
FullscreenBitsPerPixel=32
WindowedWidth=1680
WindowedHeight=1050
The 0 in FullscreenRefreshRate should reset it. If it's not, then set it to your desktop refresh rate.
Also, if it's off-center, just wait until you get to the server select screen and then hit ALT-Enter to make it fullscreen.
I have to add that the SoF client's eqclient.ini file is much different, so it would probably explain why there's less issues with that client. Might be something to consider if you can't get it to work.