I have got the same problem.
The Eagle-Gui is broken while running beryl as desktop-manager.
Always switching XGL and no-xgl is very annoying.
I had a similar problem with Java-Guis that could be fixed by setting an 
environment-variable: export AWT_TOOLKIT=MToolkit
Is there any similar solution for the Eagle-Program?

Best regards, 
 Tobias


** Attachment added: "Screenshot of eagle-problem"
   http://launchpadlibrarian.net/8095104/eagle_mit_beryl_problem.png

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After starting eagle the registration window has broken fonts
https://bugs.launchpad.net/bugs/60184
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