Peter-
Hmmm... those stencils should convert over just fine. If you download a
fresh copy of OmniGraffle from our ftp server and pull the stencils out of the folders inside the "InternalStencils" one, what happens?
When I did this, those stencils opened up and were installable. Graffle Pro 5.2.3 on a machine running 10.6.7...
<OmniGraffle App Package>/Contents/Resources/English.lproj/InternalStencils