Like all of you, I had a much faster VM when using the kvm-qemu from command line, compared to running it (the same VM) from libvirtd / virt-manager.
I noticed that libvirtd was not recognizing my kvm package, and was using qemu only (not using kvm kernel module) which was the reason for the huge performance difference.
This happened because libvirtd, stupidly, searches for the /usr/bin/kvm and /usr/bin/qemu-kvm files to determine if you have kvm installed on your system...
Since neither one was there, it assumed I had "normal" qemu installed, and used it to run the VMs... slowly...
ln -s /usr/bin/qemu /usr/bin/kvm
solved that problem.
Found this stuff after stumbling on this http://wiki.libvirt.org/page/Tips#Li...isor_.28KVM.29
Hope it solves your problems with virt-manager as well