First, let me say that I use xm since xl doesn't work for me (wants to start qemu even for paravirtualized guests. I will report that (again!) upstream). Now to this issue: the xen-tools ebuild messes up all shebangs. Not only /usr/bin/xm but also in xend, xen-bugtool, xsview, and whatnot. I'm not sure why. I didn't analyse the ebuild. But it's severely broken. Reproducible: Always
Fixed with the effort of the dev maker of the python-r1 eclasses, the ebuild converted to the new eclass including the fixing of the shebangs, 16th. - 17th. December
*** Bug 435888 has been marked as a duplicate of this bug. ***
How/where is this fixed? I still encountered this issue in 4.2.0-r1 today, and resorted to fixing it manually between configure and compile.