Dual Monitor alignment

I have 2 Apple Aluminum framed Apple 30" monitors. With my 2007 MacPro, the graphics card supported two DVI attachments. The monitors were aligned...a window spanning both monitors was perfectly straight. My new 2010 MacPro (with the ATI Radeon HD 5870 graphics card) supports only one DVI connection so I bought an Apple mini-display to dual-link DVI adaptor. It works fine but the monitors are no longer aligned; a window spanning both monitors is no longer straight. The monitor supported by the adaptor is roughly 20% lower. Any ideas?

Open System Preferences > Displays ...
And adjust the two Icon images of your displays (each is proportional in size to the number of pixels on each display) to your liking. To mirror instead of Extended Desktop, drag one on top of the other. To go back to Extended desktop, drag them apart and position them to your liking.
While there, you can also drag the MenuBar from one display to the other.

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