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It’s possible the Alt key is not where you think it is or is defined incorrectly. Try running the GSTest application, KeyboardInput test (located in the examples package at ftp://ftp.gnustep.org/pub/gnustep/core) to test it. See http://www.gnustep.org/resources/documentation/User/Gui/KeyboardSetup.html for information on how to change the settings.
If you are using WindowMaker, it’s possible it is grabing this key and using it for itself. To check, open Window Maker’s WPrefs and go to the Mouse Preferences. Then use another value for the "Mouse grab modifier" (bottom right). That will allow you to alt-drag things.