I can confirm that i also encounter this issue on Fedora 17 and Fedora 18.
following the following directions from comment #8 here fixed the issue for me:
https://bbs.archlinux.org/viewtopic.php?pid=876274#p876274
Although i updated lwjgl to the most recent stable release, (lwjgl-2.8.5), following these directions updated it and now works when more than one monitor is connected on Linux.
Is there any way to get lwjgl updated in the minecraft launcher?
Just downloaded a fresh minecraft.jar, deleted "~/.minecraft" and ran minecraft again, and still getting the issue.
regards,
ryanlerch