ReactomePA pathway plots generated using viewPathway seem to be missing components of the pathway.
For example if you view the human "HDL-mediated lipid transport" using viewPathway, the resulting network has 14 nodes. However, if you get any of the pathway mapping files from the reactome website, the "HDL-meidated lipid transport" pathway in humans has 19 members. So for example the genes "ALB", "HDLBP" and "PLTP" are listed as being members in the NCBI2pathway mapping from the reactome website, and on the website webapp, but don't appear on pathView.
I've tracked down that ReactomePA pulls its Reactome data from graphite, and that when you pull the "HDL-mediated lipid transport" out of graphite, it does indeed only contain these 14 genes (actaully they are UniProt IDs in graphite). The data retrieved is marked as 12-10-2016, so it seems unlikely that the data is stale.
Any idea where this data came from, and why its different to that on the website.