Change the DESTINATION to lib/vdpau .

# pkgfile -rv lib/vdpau
extra/ati-dri 9.1.2-1            	/usr/lib/vdpau/libvdpau_r600.so.1.0.0
extra/ati-dri 9.1.2-1            	/usr/lib/vdpau/libvdpau_r300.so
extra/ati-dri 9.1.2-1            	/usr/lib/vdpau/libvdpau_r300.so.1.0.0
extra/ati-dri 9.1.2-1            	/usr/lib/vdpau/libvdpau_radeonsi.so.1.0.0
extra/ati-dri 9.1.2-1            	/usr/lib/vdpau/libvdpau_r600.so.1
extra/ati-dri 9.1.2-1            	/usr/lib/vdpau/libvdpau_radeonsi.so.1
extra/ati-dri 9.1.2-1            	/usr/lib/vdpau/libvdpau_r300.so.1
extra/ati-dri 9.1.2-1            	/usr/lib/vdpau/libvdpau_radeonsi.so
extra/ati-dri 9.1.2-1            	/usr/lib/vdpau/libvdpau_r600.so
extra/libvdpau 0.6-1             	/usr/lib/vdpau/libvdpau_trace.so.1.0.0
extra/libvdpau 0.6-1             	/usr/lib/vdpau/libvdpau_trace.so.1
extra/libvdpau 0.6-1             	/usr/lib/vdpau/libvdpau_trace.so
extra/mesa 9.1.2-1               	/usr/lib/vdpau/libvdpau_softpipe.so.1
extra/mesa 9.1.2-1               	/usr/lib/vdpau/libvdpau_softpipe.so.1.0.0
extra/mesa 9.1.2-1               	/usr/lib/vdpau/libvdpau_softpipe.so
extra/nouveau-dri 9.1.2-1        	/usr/lib/vdpau/libvdpau_nouveau.so
extra/nouveau-dri 9.1.2-1        	/usr/lib/vdpau/libvdpau_nouveau.so.1
extra/nouveau-dri 9.1.2-1        	/usr/lib/vdpau/libvdpau_nouveau.so.1.0.0
extra/nvidia-304xx-utils 304.88-1	/usr/lib/vdpau/libvdpau_nvidia.so.1
extra/nvidia-304xx-utils 304.88-1	/usr/lib/vdpau/libvdpau_nvidia.so.304.88
extra/nvidia-304xx-utils 304.88-1	/usr/lib/vdpau/libvdpau_nvidia.so
extra/nvidia-utils 319.17-1      	/usr/lib/vdpau/libvdpau_nvidia.so
extra/nvidia-utils 319.17-1      	/usr/lib/vdpau/libvdpau_nvidia.so.319.17
extra/nvidia-utils 319.17-1      	/usr/lib/vdpau/libvdpau_nvidia.so.1