It appears that some of the links in the help pages refer to version 5 rather than 5.1. You don't notice this until you remove 5.0 (and its help content). All the links I have tested in the left-side navigation frames work OK. The broken links always appear in the main content frame.
Two links are below; note the difference in the productVersion parameter between the two:
This one works:
This one is broken:
(ATTicket:669117)